0	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	\N	sequence	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SO	42237	SO:0000001	\N	region	SO:0000001
0	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A folded sequence." [SO:ke]	SO	42238	SO:0000002	\N	sequence_secondary_structure	SO:0000002
0	"G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]	\N	G_quartet	\N	\N	sequence	"G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]	SO	42239	SO:0000003	\N	G_quartet	SO:0000003
0	"" []	SOFA	interior_coding_exon	SOFA	\N	sequence	"" []	SO	42240	SO:0000004	\N	interior_coding_exon	SO:0000004
0	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	satellite_DNA	SOFA	\N	sequence	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42241	SO:0000005	\N	satellite_DNA	SO:0000005
0	"A region amplified by a PCR reaction." [SO:ke]	SOFA	PCR_product	SOFA	\N	sequence	"A region amplified by a PCR reaction." [SO:ke]	SO	42242	SO:0000006	\N	PCR_product	SO:0000006
0	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SOFA	read_pair	SOFA	\N	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	42243	SO:0000007	\N	read_pair	SO:0000007
0	"" []	\N	protein_coding	\N	\N	sequence	"" []	SO	42244	SO:0000010	\N	protein_coding	SO:0000010
0	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	42245	SO:0000011	\N	non_protein_coding	SO:0000011
0	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	\N	scRNA_primary_transcript	\N	\N	sequence	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	SO	42246	SO:0000012	\N	scRNA_primary_transcript	SO:0000012
0	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SOFA	scRNA	SOFA	\N	sequence	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SO	42247	SO:0000013	\N	scRNA	SO:0000013
0	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	\N	INR_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	42248	SO:0000014	\N	INR_motif	SO:0000014
0	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	\N	DPE_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	42249	SO:0000015	\N	DPE_motif	SO:0000015
0	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	\N	BREu_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	42250	SO:0000016	\N	BREu_motif	SO:0000016
0	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	\N	PSE_motif	\N	\N	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	42251	SO:0000017	\N	PSE_motif	SO:0000017
0	"A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]	\N	linkage_group	\N	\N	sequence	"A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]	SO	42252	SO:0000018	\N	linkage_group	SO:0000018
0	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	\N	RNA_internal_loop	\N	\N	sequence	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	SO	42253	SO:0000020	\N	RNA_internal_loop	SO:0000020
0	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	\N	asymmetric_RNA_internal_loop	\N	\N	sequence	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	SO	42254	SO:0000021	\N	asymmetric_RNA_internal_loop	SO:0000021
0	"A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]	\N	A_minor_RNA_motif	\N	\N	sequence	"A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]	SO	42255	SO:0000022	\N	A_minor_RNA_motif	SO:0000022
0	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	\N	K_turn_RNA_motif	\N	\N	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	42256	SO:0000023	\N	K_turn_RNA_motif	SO:0000023
0	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	\N	sarcin_like_RNA_motif	\N	\N	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	42257	SO:0000024	\N	sarcin_like_RNA_motif	SO:0000024
0	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	\N	symmetric_RNA_internal_loop	\N	\N	sequence	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	SO	42258	SO:0000025	\N	symmetric_RNA_internal_loop	SO:0000025
0	"" []	\N	RNA_junction_loop	\N	\N	sequence	"" []	SO	42259	SO:0000026	\N	RNA_junction_loop	SO:0000026
0	"" []	\N	RNA_hook_turn	\N	\N	sequence	"" []	SO	42260	SO:0000027	\N	RNA_hook_turn	SO:0000027
0	"" []	\N	base_pair	\N	\N	sequence	"" []	SO	42261	SO:0000028	\N	base_pair	SO:0000028
0	"The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]	\N	WC_base_pair	\N	\N	sequence	"The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]	SO	42262	SO:0000029	\N	WC_base_pair	SO:0000029
0	"A type of non-canonical base-pairing." [PMID:12177293]	\N	sugar_edge_base_pair	\N	\N	sequence	"A type of non-canonical base-pairing." [PMID:12177293]	SO	42263	SO:0000030	\N	sugar_edge_base_pair	SO:0000030
0	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	\N	aptamer	\N	\N	sequence	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	42264	SO:0000031	\N	aptamer	SO:0000031
0	"DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]	\N	DNA_aptamer	\N	\N	sequence	"DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]	SO	42265	SO:0000032	\N	DNA_aptamer	SO:0000032
0	"RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	\N	RNA_aptamer	\N	\N	sequence	"RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	42266	SO:0000033	\N	RNA_aptamer	SO:0000033
0	"Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]	\N	morpholino_oligo	\N	\N	sequence	"Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]	SO	42267	SO:0000034	\N	morpholino_oligo	SO:0000034
0	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	\N	riboswitch	\N	\N	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	42268	SO:0000035	\N	riboswitch	SO:0000035
0	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	\N	matrix_attachment_site	\N	\N	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	42269	SO:0000036	\N	matrix_attachment_site	SO:0000036
0	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	\N	locus_control_region	\N	\N	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	42270	SO:0000037	\N	locus_control_region	SO:0000037
0	"A part of a match, for example an hsp from blast is a match_part." [SO:ke]	SOFA	match_part	SOFA	\N	sequence	"A part of a match, for example an hsp from blast is a match_part." [SO:ke]	SO	42271	SO:0000039	\N	match_part	SO:0000039
0	"A clone of a DNA region of a genome." [SO:ma]	\N	genomic_clone	\N	\N	sequence	"A clone of a DNA region of a genome." [SO:ma]	SO	42272	SO:0000040	\N	genomic_clone	SO:0000040
0	"A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]	\N	processed_pseudogene	\N	\N	sequence	"A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]	SO	42273	SO:0000043	\N	processed_pseudogene	SO:0000043
0	"A pseudogene caused by unequal crossing over at recombination." [SO:ke]	\N	pseudogene_by_unequal_crossing_over	\N	\N	sequence	"A pseudogene caused by unequal crossing over at recombination." [SO:ke]	SO	42274	SO:0000044	\N	pseudogene_by_unequal_crossing_over	SO:0000044
0	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	\N	probe	\N	\N	sequence	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	SO	42275	SO:0000051	\N	probe	SO:0000051
0	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	aneuploid	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	42276	SO:0000054	\N	aneuploid	SO:0000054
0	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	\N	hyperploid	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	42277	SO:0000055	\N	hyperploid	SO:0000055
0	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	\N	hypoploid	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	42278	SO:0000056	\N	hypoploid	SO:0000056
0	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SOFA	operator	SOFA	\N	sequence	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SO	42279	SO:0000057	\N	operator	SO:0000057
0	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SOFA	nuclease_binding_site	SOFA	\N	sequence	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SO	42280	SO:0000059	\N	nuclease_binding_site	SO:0000059
0	"" []	\N	compound_chromosome_arm	\N	\N	sequence	"" []	SO	42281	SO:0000060	\N	compound_chromosome_arm	SO:0000060
0	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	\N	restriction_enzyme_binding_site	\N	\N	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	SO	42282	SO:0000061	\N	restriction_enzyme_binding_site	SO:0000061
0	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	\N	deficient_intrachromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	42283	SO:0000062	\N	deficient_intrachromosomal_transposition	SO:0000062
0	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	\N	deficient_interchromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	42284	SO:0000063	\N	deficient_interchromosomal_transposition	SO:0000063
0	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	\N	free_chromosome_arm	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	42285	SO:0000065	\N	free_chromosome_arm	SO:0000065
0	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"" []	SO	42286	SO:0000067	\N	gene_to_gene_feature	SO:0000067
0	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	SO	42287	SO:0000068	\N	overlapping	SO:0000068
0	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	\N	inside_intron	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	SO	42288	SO:0000069	\N	inside_intron	SO:0000069
0	"An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]	\N	inside_intron_antiparallel	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]	SO	42289	SO:0000070	\N	inside_intron_antiparallel	SO:0000070
0	"An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]	\N	inside_intron_parallel	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]	SO	42290	SO:0000071	\N	inside_intron_parallel	SO:0000071
0	"An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]	\N	five_prime_three_prime_overlap	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]	SO	42291	SO:0000073	\N	five_prime_three_prime_overlap	SO:0000073
0	"An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]	\N	five_prime_five_prime_overlap	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]	SO	42292	SO:0000074	\N	five_prime_five_prime_overlap	SO:0000074
0	"An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]	\N	three_prime_three_prime_overlap	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]	SO	42293	SO:0000075	\N	three_prime_three_prime_overlap	SO:0000075
0	"An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]	\N	three_prime_five_prime_overlap	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]	SO	42294	SO:0000076	\N	three_prime_five_prime_overlap	SO:0000076
0	"A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]	\N	antisense	\N	\N	sequence	"A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]	SO	42295	SO:0000077	\N	antisense	SO:0000077
0	"A transcript that is polycistronic." [SO:xp]	\N	polycistronic_transcript	\N	\N	sequence	"A transcript that is polycistronic." [SO:xp]	SO	42296	SO:0000078	\N	polycistronic_transcript	SO:0000078
0	"A transcript that is dicistronic." [SO:ke]	\N	dicistronic_transcript	\N	\N	sequence	"A transcript that is dicistronic." [SO:ke]	SO	42297	SO:0000079	\N	dicistronic_transcript	SO:0000079
0	"" []	\N	operon_member	\N	\N	sequence	"" []	SO	42298	SO:0000080	\N	operon_member	SO:0000080
0	"" []	\N	gene_array_member	\N	\N	sequence	"" []	SO	42299	SO:0000081	\N	gene_array_member	SO:0000081
0	"" []	\N	macronuclear_sequence	\N	\N	sequence	"" []	SO	42300	SO:0000083	\N	macronuclear_sequence	SO:0000083
0	"" []	\N	micronuclear_sequence	\N	\N	sequence	"" []	SO	42301	SO:0000084	\N	micronuclear_sequence	SO:0000084
0	"A gene from nuclear sequence." [SO:xp]	\N	nuclear_gene	\N	\N	sequence	"A gene from nuclear sequence." [SO:xp]	SO	42302	SO:0000087	\N	nuclear_gene	SO:0000087
0	"A gene located in mitochondrial sequence." [SO:xp]	\N	mt_gene	\N	\N	sequence	"A gene located in mitochondrial sequence." [SO:xp]	SO	42303	SO:0000088	\N	mt_gene	SO:0000088
0	"A gene located in kinetoplast sequence." [SO:xp]	\N	kinetoplast_gene	\N	\N	sequence	"A gene located in kinetoplast sequence." [SO:xp]	SO	42304	SO:0000089	\N	kinetoplast_gene	SO:0000089
0	"A gene from plastid sequence." [SO:xp]	\N	plastid_gene	\N	\N	sequence	"A gene from plastid sequence." [SO:xp]	SO	42305	SO:0000090	\N	plastid_gene	SO:0000090
0	"A gene from apicoplast sequence." [SO:xp]	\N	apicoplast_gene	\N	\N	sequence	"A gene from apicoplast sequence." [SO:xp]	SO	42306	SO:0000091	\N	apicoplast_gene	SO:0000091
0	"A gene from chloroplast sequence." [SO:xp]	\N	ct_gene	\N	\N	sequence	"A gene from chloroplast sequence." [SO:xp]	SO	42307	SO:0000092	\N	ct_gene	SO:0000092
0	"A gene from chromoplast_sequence." [SO:xp]	\N	chromoplast_gene	\N	\N	sequence	"A gene from chromoplast_sequence." [SO:xp]	SO	42308	SO:0000093	\N	chromoplast_gene	SO:0000093
0	"A gene from cyanelle sequence." [SO:xp]	\N	cyanelle_gene	\N	\N	sequence	"A gene from cyanelle sequence." [SO:xp]	SO	42309	SO:0000094	\N	cyanelle_gene	SO:0000094
0	"A plastid gene from leucoplast sequence." [SO:xp]	\N	leucoplast_gene	\N	\N	sequence	"A plastid gene from leucoplast sequence." [SO:xp]	SO	42310	SO:0000095	\N	leucoplast_gene	SO:0000095
0	"A gene from proplastid sequence." [SO:ke]	\N	proplastid_gene	\N	\N	sequence	"A gene from proplastid sequence." [SO:ke]	SO	42311	SO:0000096	\N	proplastid_gene	SO:0000096
0	"A gene from nucleomorph sequence." [SO:xp]	\N	nucleomorph_gene	\N	\N	sequence	"A gene from nucleomorph sequence." [SO:xp]	SO	42312	SO:0000097	\N	nucleomorph_gene	SO:0000097
0	"A gene from plasmid sequence." [SO:xp]	\N	plasmid_gene	\N	\N	sequence	"A gene from plasmid sequence." [SO:xp]	SO	42313	SO:0000098	\N	plasmid_gene	SO:0000098
0	"A gene from proviral sequence." [SO:xp]	\N	proviral_gene	\N	\N	sequence	"A gene from proviral sequence." [SO:xp]	SO	42314	SO:0000099	\N	proviral_gene	SO:0000099
0	"A proviral gene with origin endogenous retrovirus." [SO:xp]	\N	endogenous_retroviral_gene	\N	\N	sequence	"A proviral gene with origin endogenous retrovirus." [SO:xp]	SO	42315	SO:0000100	\N	endogenous_retroviral_gene	SO:0000100
0	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	SOFA	transposable_element	SOFA	\N	sequence	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	SO	42316	SO:0000101	\N	transposable_element	SO:0000101
0	"A match to an EST or cDNA sequence." [SO:ke]	SOFA	expressed_sequence_match	SOFA	\N	sequence	"A match to an EST or cDNA sequence." [SO:ke]	SO	42317	SO:0000102	\N	expressed_sequence_match	SO:0000102
0	"The end of the clone insert." [SO:ke]	SOFA	clone_insert_end	SOFA	\N	sequence	"The end of the clone insert." [SO:ke]	SO	42318	SO:0000103	\N	clone_insert_end	SO:0000103
0	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	SOFA	polypeptide	SOFA	\N	sequence	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	SO	42319	SO:0000104	\N	polypeptide	SO:0000104
0	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	\N	chromosome_arm	\N	\N	sequence	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	SO	42320	SO:0000105	\N	chromosome_arm	SO:0000105
0	"" []	\N	sequencing_primer	\N	\N	sequence	"" []	SO	42321	SO:0000107	\N	sequencing_primer	SO:0000107
0	"An mRNA with a frameshift." [SO:xp]	\N	mRNA_with_frameshift	\N	\N	sequence	"An mRNA with a frameshift." [SO:xp]	SO	42322	SO:0000108	\N	mRNA_with_frameshift	SO:0000108
0	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	\N	sequence	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SO	42323	SO:0000110	\N	sequence_feature	SO:0000110
0	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	\N	transposable_element_gene	\N	\N	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	42324	SO:0000111	\N	transposable_element_gene	SO:0000111
0	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	SOFA	primer	SOFA	\N	sequence	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	SO	42325	SO:0000112	\N	primer	SO:0000112
0	"A viral sequence which has integrated into a host genome." [SO:ke]	SOFA	proviral_region	SOFA	\N	sequence	"A viral sequence which has integrated into a host genome." [SO:ke]	SO	42326	SO:0000113	\N	proviral_region	SO:0000113
0	"A methylated deoxy-cytosine." [SO:ke]	SOFA	methylated_cytosine	SOFA	\N	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	42327	SO:0000114	\N	methylated_cytosine	SO:0000114
0	"An attribute describing a sequence that is modified by editing." [SO:ke]	\N	edited	\N	\N	sequence	"An attribute describing a sequence that is modified by editing." [SO:ke]	SO	42328	SO:0000116	\N	edited	SO:0000116
0	"A transcript with a translational frameshift." [SO:xp]	\N	transcript_with_translational_frameshift	\N	\N	sequence	"A transcript with a translational frameshift." [SO:xp]	SO	42329	SO:0000118	\N	transcript_with_translational_frameshift	SO:0000118
0	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute to describe a sequence that is regulated." [SO:ke]	SO	42330	SO:0000119	\N	regulated	SO:0000119
0	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	SOFA	protein_coding_primary_transcript	SOFA	\N	sequence	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	SO	42331	SO:0000120	\N	protein_coding_primary_transcript	SO:0000120
0	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	\N	forward_primer	\N	\N	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	42332	SO:0000121	\N	forward_primer	SO:0000121
0	"A folded RNA sequence." [SO:ke]	\N	RNA_sequence_secondary_structure	\N	\N	sequence	"A folded RNA sequence." [SO:ke]	SO	42333	SO:0000122	\N	RNA_sequence_secondary_structure	SO:0000122
0	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An attribute describing a gene that is regulated at transcription." [SO:ma]	SO	42334	SO:0000123	\N	transcriptionally_regulated	SO:0000123
0	"Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]	\N	transcriptionally_constitutive	\N	\N	sequence	"Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]	SO	42335	SO:0000124	\N	transcriptionally_constitutive	SO:0000124
0	"An inducer molecule is required for transcription to occur." [SO:ke]	\N	transcriptionally_induced	\N	\N	sequence	"An inducer molecule is required for transcription to occur." [SO:ke]	SO	42336	SO:0000125	\N	transcriptionally_induced	SO:0000125
0	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"A repressor molecule is required for transcription to stop." [SO:ke]	SO	42337	SO:0000126	\N	transcriptionally_repressed	SO:0000126
0	"A gene that is silenced." [SO:xp]	\N	silenced_gene	\N	\N	sequence	"A gene that is silenced." [SO:xp]	SO	42338	SO:0000127	\N	silenced_gene	SO:0000127
0	"A gene that is silenced by DNA modification." [SO:xp]	\N	gene_silenced_by_DNA_modification	\N	\N	sequence	"A gene that is silenced by DNA modification." [SO:xp]	SO	42339	SO:0000128	\N	gene_silenced_by_DNA_modification	SO:0000128
0	"A gene that is silenced by DNA methylation." [SO:xp]	\N	gene_silenced_by_DNA_methylation	\N	\N	sequence	"A gene that is silenced by DNA methylation." [SO:xp]	SO	42340	SO:0000129	\N	gene_silenced_by_DNA_methylation	SO:0000129
0	"An attribute describing a gene that is regulated after it has been translated." [SO:ke]	\N	post_translationally_regulated	\N	\N	sequence	"An attribute describing a gene that is regulated after it has been translated." [SO:ke]	SO	42341	SO:0000130	\N	post_translationally_regulated	SO:0000130
0	"An attribute describing a gene that is regulated as it is translated." [SO:ke]	\N	translationally_regulated	\N	\N	sequence	"An attribute describing a gene that is regulated as it is translated." [SO:ke]	SO	42342	SO:0000131	\N	translationally_regulated	SO:0000131
0	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	\N	reverse_primer	\N	\N	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	42343	SO:0000132	\N	reverse_primer	SO:0000132
0	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	\N	epigenetically_modified	\N	\N	sequence	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	SO	42344	SO:0000133	\N	epigenetically_modified	SO:0000133
0	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	\N	genomically_imprinted	\N	\N	sequence	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	SO	42345	SO:0000134	\N	genomically_imprinted	SO:0000134
0	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	\N	maternally_imprinted	\N	\N	sequence	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	42346	SO:0000135	\N	maternally_imprinted	SO:0000135
0	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	\N	paternally_imprinted	\N	\N	sequence	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	42347	SO:0000136	\N	paternally_imprinted	SO:0000136
0	"Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]	\N	allelically_excluded	\N	\N	sequence	"Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]	SO	42348	SO:0000137	\N	allelically_excluded	SO:0000137
0	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	\N	gene_rearranged_at_DNA_level	\N	\N	sequence	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	SO	42349	SO:0000138	\N	gene_rearranged_at_DNA_level	SO:0000138
0	"Region in mRNA where ribosome assembles." [SO:ke]	SOFA	ribosome_entry_site	SOFA	\N	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	42350	SO:0000139	\N	ribosome_entry_site	SO:0000139
0	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SOFA	attenuator	SOFA	\N	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	42351	SO:0000140	\N	attenuator	SO:0000140
0	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	terminator	SOFA	\N	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42352	SO:0000141	\N	terminator	SO:0000141
0	"A folded DNA sequence." [SO:ke]	\N	DNA_sequence_secondary_structure	\N	\N	sequence	"A folded DNA sequence." [SO:ke]	SO	42353	SO:0000142	\N	DNA_sequence_secondary_structure	SO:0000142
0	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	\N	sequence	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SO	42354	SO:0000143	\N	assembly_component	SO:0000143
0	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	\N	recoded_codon	\N	\N	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	42355	SO:0000145	\N	recoded_codon	SO:0000145
0	"An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke]	\N	capped	\N	\N	sequence	"An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke]	SO	42356	SO:0000146	\N	capped	SO:0000146
0	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	\N	sequence	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SO	42357	SO:0000147	\N	exon	SO:0000147
0	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SOFA	supercontig	SOFA	\N	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	42358	SO:0000148	\N	supercontig	SO:0000148
0	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SOFA	contig	SOFA	\N	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	42359	SO:0000149	\N	contig	SO:0000149
0	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SOFA	read	SOFA	\N	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	42360	SO:0000150	\N	read	SO:0000150
0	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SOFA	clone	SOFA	\N	sequence	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SO	42361	SO:0000151	\N	clone	SO:0000151
0	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	\N	YAC	\N	\N	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	42362	SO:0000152	\N	YAC	SO:0000152
0	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	\N	BAC	\N	\N	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	42363	SO:0000153	\N	BAC	SO:0000153
0	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	\N	PAC	\N	\N	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	42364	SO:0000154	\N	PAC	SO:0000154
0	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	SO	42365	SO:0000155	\N	plasmid	SO:0000155
0	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	\N	cosmid	\N	\N	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	42366	SO:0000156	\N	cosmid	SO:0000156
0	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	\N	phagemid	\N	\N	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	42367	SO:0000157	\N	phagemid	SO:0000157
0	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	\N	fosmid	\N	\N	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	42368	SO:0000158	\N	fosmid	SO:0000158
0	"The point at which one or more contiguous nucleotides were excised." [SO:ke]	SOFA	deletion	SOFA	\N	sequence	"The point at which one or more contiguous nucleotides were excised." [SO:ke]	SO	42369	SO:0000159	\N	deletion	SO:0000159
0	"A modified  base in which adenine has been methylated." [SO:ke]	SOFA	methylated_adenine	SOFA	\N	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	42370	SO:0000161	\N	methylated_adenine	SO:0000161
0	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SOFA	splice_site	SOFA	\N	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	42371	SO:0000162	\N	splice_site	SO:0000162
0	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SOFA	five_prime_cis_splice_site	SOFA	\N	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	42372	SO:0000163	\N	five_prime_cis_splice_site	SO:0000163
0	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SOFA	three_prime_cis_splice_site	SOFA	\N	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	42373	SO:0000164	\N	three_prime_cis_splice_site	SO:0000164
0	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	enhancer	SOFA	\N	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42374	SO:0000165	\N	enhancer	SO:0000165
0	"An enhancer bound by a factor." [SO:xp]	\N	enhancer_bound_by_factor	\N	\N	sequence	"An enhancer bound by a factor." [SO:xp]	SO	42375	SO:0000166	\N	enhancer_bound_by_factor	SO:0000166
0	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SOFA	promoter	SOFA	\N	sequence	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SO	42376	SO:0000167	\N	promoter	SO:0000167
0	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	\N	RNApol_I_promoter	\N	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	42377	SO:0000169	\N	RNApol_I_promoter	SO:0000169
0	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	42378	SO:0000170	\N	RNApol_II_promoter	SO:0000170
0	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	42379	SO:0000171	\N	RNApol_III_promoter	SO:0000171
0	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	CAAT_signal	\N	\N	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42380	SO:0000172	\N	CAAT_signal	SO:0000172
0	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	GC_rich_promoter_region	\N	\N	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42381	SO:0000173	\N	GC_rich_promoter_region	SO:0000173
0	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	\N	TATA_box	\N	\N	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	42382	SO:0000174	\N	TATA_box	SO:0000174
0	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	minus_10_signal	\N	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42383	SO:0000175	\N	minus_10_signal	SO:0000175
0	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	minus_35_signal	\N	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42384	SO:0000176	\N	minus_35_signal	SO:0000176
0	"A nucleotide match against a sequence from another organism." [SO:ma]	SOFA	cross_genome_match	SOFA	\N	sequence	"A nucleotide match against a sequence from another organism." [SO:ma]	SO	42385	SO:0000177	\N	cross_genome_match	SO:0000177
0	"A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]	SOFA	operon	SOFA	\N	sequence	"A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]	SO	42386	SO:0000178	\N	operon	SO:0000178
0	"The start of the clone insert." [SO:ke]	SOFA	clone_insert_start	SOFA	\N	sequence	"The start of the clone insert." [SO:ke]	SO	42387	SO:0000179	\N	clone_insert_start	SO:0000179
0	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	SO	42388	SO:0000180	\N	retrotransposon	SO:0000180
0	"A match against a translated sequence." [SO:ke]	SOFA	translated_nucleotide_match	SOFA	\N	sequence	"A match against a translated sequence." [SO:ke]	SO	42389	SO:0000181	\N	translated_nucleotide_match	SO:0000181
0	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	SO	42390	SO:0000182	\N	DNA_transposon	SO:0000182
0	"A region of the gene which is not transcribed." [SO:ke]	SOFA	non_transcribed_region	SOFA	\N	sequence	"A region of the gene which is not transcribed." [SO:ke]	SO	42391	SO:0000183	\N	non_transcribed_region	SO:0000183
0	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	\N	U2_intron	\N	\N	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	42392	SO:0000184	\N	U2_intron	SO:0000184
0	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	\N	sequence	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SO	42393	SO:0000185	\N	primary_transcript	SO:0000185
0	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	42394	SO:0000186	\N	LTR_retrotransposon	SO:0000186
0	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	intron	SOFA	\N	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42395	SO:0000188	\N	intron	SO:0000188
0	"A retrotransposon without long terminal repeat sequences." [SO:ke]	\N	non_LTR_retrotransposon	\N	\N	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	42396	SO:0000189	\N	non_LTR_retrotransposon	SO:0000189
0	"" []	\N	five_prime_intron	\N	\N	sequence	"" []	SO	42397	SO:0000190	\N	five_prime_intron	SO:0000190
0	"" []	\N	interior_intron	\N	\N	sequence	"" []	SO	42398	SO:0000191	\N	interior_intron	SO:0000191
0	"" []	\N	three_prime_intron	\N	\N	sequence	"" []	SO	42399	SO:0000192	\N	three_prime_intron	SO:0000192
0	"A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]	SOFA	RFLP_fragment	SOFA	\N	sequence	"A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]	SO	42400	SO:0000193	\N	RFLP_fragment	SO:0000193
0	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	LINE_element	\N	\N	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	42401	SO:0000194	\N	LINE_element	SO:0000194
0	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SOFA	coding_exon	SOFA	\N	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	42402	SO:0000195	\N	coding_exon	SO:0000195
0	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SOFA	five_prime_coding_exon_coding_region	SOFA	\N	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	42403	SO:0000196	\N	five_prime_coding_exon_coding_region	SO:0000196
0	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SOFA	three_prime_coding_exon_coding_region	SOFA	\N	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	42404	SO:0000197	\N	three_prime_coding_exon_coding_region	SO:0000197
0	"An exon that does not contain any codons." [SO:ke]	SOFA	noncoding_exon	SOFA	\N	sequence	"An exon that does not contain any codons." [SO:ke]	SO	42405	SO:0000198	\N	noncoding_exon	SO:0000198
0	"A region of nucleotide sequence that has translocated to a new position." [SO:ke]	DBVAR	translocation	DBVAR	\N	sequence	"A region of nucleotide sequence that has translocated to a new position." [SO:ke]	SO	42406	SO:0000199	\N	translocation	SO:0000199
0	"The 5' most coding exon." [SO:ke]	SOFA	five_prime_coding_exon	SOFA	\N	sequence	"The 5' most coding exon." [SO:ke]	SO	42407	SO:0000200	\N	five_prime_coding_exon	SO:0000200
0	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	\N	interior_exon	\N	\N	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	42408	SO:0000201	\N	interior_exon	SO:0000201
0	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	\N	three_prime_coding_exon	\N	\N	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	42409	SO:0000202	\N	three_prime_coding_exon	SO:0000202
0	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SOFA	UTR	SOFA	\N	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	42410	SO:0000203	\N	UTR	SO:0000203
0	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	five_prime_UTR	SOFA	\N	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42411	SO:0000204	\N	five_prime_UTR	SO:0000204
0	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	three_prime_UTR	SOFA	\N	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42412	SO:0000205	\N	three_prime_UTR	SO:0000205
0	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	\N	SINE_element	\N	\N	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	42413	SO:0000206	\N	SINE_element	SO:0000206
0	"" []	\N	simple_sequence_length_variation	\N	\N	sequence	"" []	SO	42414	SO:0000207	\N	simple_sequence_length_variation	SO:0000207
0	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	\N	terminal_inverted_repeat_element	\N	\N	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	42415	SO:0000208	\N	terminal_inverted_repeat_element	SO:0000208
0	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SOFA	rRNA_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SO	42416	SO:0000209	\N	rRNA_primary_transcript	SO:0000209
0	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	SO	42417	SO:0000210	\N	tRNA_primary_transcript	SO:0000210
0	"A primary transcript encoding alanyl tRNA." [SO:ke]	\N	alanine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	42418	SO:0000211	\N	alanine_tRNA_primary_transcript	SO:0000211
0	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	\N	arginine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	42419	SO:0000212	\N	arginine_tRNA_primary_transcript	SO:0000212
0	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	\N	asparagine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	42420	SO:0000213	\N	asparagine_tRNA_primary_transcript	SO:0000213
0	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	\N	aspartic_acid_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	42421	SO:0000214	\N	aspartic_acid_tRNA_primary_transcript	SO:0000214
0	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	\N	cysteine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	42422	SO:0000215	\N	cysteine_tRNA_primary_transcript	SO:0000215
0	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	\N	glutamic_acid_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	42423	SO:0000216	\N	glutamic_acid_tRNA_primary_transcript	SO:0000216
0	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	\N	glutamine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	42424	SO:0000217	\N	glutamine_tRNA_primary_transcript	SO:0000217
0	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	\N	glycine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	42425	SO:0000218	\N	glycine_tRNA_primary_transcript	SO:0000218
0	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	\N	histidine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	42426	SO:0000219	\N	histidine_tRNA_primary_transcript	SO:0000219
0	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	\N	isoleucine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	42427	SO:0000220	\N	isoleucine_tRNA_primary_transcript	SO:0000220
0	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	\N	leucine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	42428	SO:0000221	\N	leucine_tRNA_primary_transcript	SO:0000221
0	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	\N	lysine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	42429	SO:0000222	\N	lysine_tRNA_primary_transcript	SO:0000222
0	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	\N	methionine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	42430	SO:0000223	\N	methionine_tRNA_primary_transcript	SO:0000223
0	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	\N	phenylalanine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	42431	SO:0000224	\N	phenylalanine_tRNA_primary_transcript	SO:0000224
0	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	\N	proline_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	42432	SO:0000225	\N	proline_tRNA_primary_transcript	SO:0000225
0	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	\N	serine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	42433	SO:0000226	\N	serine_tRNA_primary_transcript	SO:0000226
0	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	\N	threonine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	42434	SO:0000227	\N	threonine_tRNA_primary_transcript	SO:0000227
0	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	\N	tryptophan_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	42435	SO:0000228	\N	tryptophan_tRNA_primary_transcript	SO:0000228
0	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	\N	tyrosine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	42436	SO:0000229	\N	tyrosine_tRNA_primary_transcript	SO:0000229
0	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	\N	valine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	42437	SO:0000230	\N	valine_tRNA_primary_transcript	SO:0000230
0	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	\N	snRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	SO	42438	SO:0000231	\N	snRNA_primary_transcript	SO:0000231
0	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	\N	snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	SO	42439	SO:0000232	\N	snoRNA_primary_transcript	SO:0000232
0	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	\N	sequence	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SO	42440	SO:0000233	\N	mature_transcript	SO:0000233
0	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	\N	sequence	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SO	42441	SO:0000234	\N	mRNA	SO:0000234
0	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SOFA	TF_binding_site	SOFA	\N	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	42442	SO:0000235	\N	TF_binding_site	SO:0000235
0	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	SOFA	ORF	SOFA	\N	sequence	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	SO	42443	SO:0000236	\N	ORF	SO:0000236
0	"" []	\N	transcript_attribute	\N	\N	sequence	"" []	SO	42444	SO:0000237	\N	transcript_attribute	SO:0000237
0	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	\N	foldback_element	\N	\N	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	42445	SO:0000238	\N	foldback_element	SO:0000238
0	"The sequences extending on either side of a specific region." [SO:ke]	SOFA	flanking_region	SOFA	\N	sequence	"The sequences extending on either side of a specific region." [SO:ke]	SO	42446	SO:0000239	\N	flanking_region	SO:0000239
0	"" []	\N	chromosome_variation	\N	\N	sequence	"" []	SO	42447	SO:0000240	\N	chromosome_variation	SO:0000240
0	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	\N	internal_UTR	\N	\N	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	42448	SO:0000241	\N	internal_UTR	SO:0000241
0	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	\N	untranslated_region_polycistronic_mRNA	\N	\N	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	42449	SO:0000242	\N	untranslated_region_polycistronic_mRNA	SO:0000242
0	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	\N	internal_ribosome_entry_site	\N	\N	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	42450	SO:0000243	\N	internal_ribosome_entry_site	SO:0000243
0	"A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]	\N	polyadenylated	\N	\N	sequence	"A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]	SO	42451	SO:0000246	\N	polyadenylated	SO:0000246
0	"" []	\N	sequence_length_variation	\N	\N	sequence	"" []	SO	42452	SO:0000248	\N	sequence_length_variation	SO:0000248
0	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A post_transcriptionally modified base." [SO:ke]	SO	42453	SO:0000250	\N	modified_RNA_base_feature	SO:0000250
0	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	\N	sequence	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SO	42454	SO:0000252	\N	rRNA	SO:0000252
0	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SOFA	tRNA	SOFA	\N	sequence	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SO	42455	SO:0000253	\N	tRNA	SO:0000253
0	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	\N	alanyl_tRNA	\N	\N	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	42456	SO:0000254	\N	alanyl_tRNA	SO:0000254
0	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	\N	rRNA_small_subunit_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	42457	SO:0000255	\N	rRNA_small_subunit_primary_transcript	SO:0000255
0	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	\N	asparaginyl_tRNA	\N	\N	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	42458	SO:0000256	\N	asparaginyl_tRNA	SO:0000256
0	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	\N	aspartyl_tRNA	\N	\N	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	42459	SO:0000257	\N	aspartyl_tRNA	SO:0000257
0	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	\N	cysteinyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	42460	SO:0000258	\N	cysteinyl_tRNA	SO:0000258
0	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	\N	glutaminyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	42461	SO:0000259	\N	glutaminyl_tRNA	SO:0000259
0	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	\N	glutamyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	42462	SO:0000260	\N	glutamyl_tRNA	SO:0000260
0	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	\N	glycyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	42463	SO:0000261	\N	glycyl_tRNA	SO:0000261
0	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	\N	histidyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	42464	SO:0000262	\N	histidyl_tRNA	SO:0000262
0	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	\N	isoleucyl_tRNA	\N	\N	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	42465	SO:0000263	\N	isoleucyl_tRNA	SO:0000263
0	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	\N	leucyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	42466	SO:0000264	\N	leucyl_tRNA	SO:0000264
0	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	\N	lysyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	42467	SO:0000265	\N	lysyl_tRNA	SO:0000265
0	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	\N	methionyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	42468	SO:0000266	\N	methionyl_tRNA	SO:0000266
0	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	\N	phenylalanyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	42469	SO:0000267	\N	phenylalanyl_tRNA	SO:0000267
0	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	\N	prolyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	42470	SO:0000268	\N	prolyl_tRNA	SO:0000268
0	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	\N	seryl_tRNA	\N	\N	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	42471	SO:0000269	\N	seryl_tRNA	SO:0000269
0	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	\N	threonyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	42472	SO:0000270	\N	threonyl_tRNA	SO:0000270
0	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	\N	tryptophanyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	42473	SO:0000271	\N	tryptophanyl_tRNA	SO:0000271
0	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	\N	tyrosyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	42474	SO:0000272	\N	tyrosyl_tRNA	SO:0000272
0	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	\N	valyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	42475	SO:0000273	\N	valyl_tRNA	SO:0000273
0	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	\N	sequence	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SO	42476	SO:0000274	\N	snRNA	SO:0000274
0	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SOFA	snoRNA	SOFA	\N	sequence	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SO	42477	SO:0000275	\N	snoRNA	SO:0000275
0	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SOFA	miRNA	SOFA	\N	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	42478	SO:0000276	\N	miRNA	SO:0000276
0	"An attribute describing a sequence that is bound by another molecule." [SO:ke]	\N	bound_by_factor	\N	\N	sequence	"An attribute describing a sequence that is bound by another molecule." [SO:ke]	SO	42479	SO:0000277	\N	bound_by_factor	SO:0000277
0	"A transcript that is bound by a nucleic acid." [SO:xp]	\N	transcript_bound_by_nucleic_acid	\N	\N	sequence	"A transcript that is bound by a nucleic acid." [SO:xp]	SO	42480	SO:0000278	\N	transcript_bound_by_nucleic_acid	SO:0000278
0	"A transcript that is bound by a protein." [SO:xp]	\N	transcript_bound_by_protein	\N	\N	sequence	"A transcript that is bound by a protein." [SO:xp]	SO	42481	SO:0000279	\N	transcript_bound_by_protein	SO:0000279
0	"A gene that is engineered." [SO:xp]	\N	engineered_gene	\N	\N	sequence	"A gene that is engineered." [SO:xp]	SO	42482	SO:0000280	\N	engineered_gene	SO:0000280
0	"A gene that is engineered and foreign." [SO:xp]	\N	engineered_foreign_gene	\N	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	42483	SO:0000281	\N	engineered_foreign_gene	SO:0000281
0	"An mRNA with a minus 1 frameshift." [SO:xp]	\N	mRNA_with_minus_1_frameshift	\N	\N	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	42484	SO:0000282	\N	mRNA_with_minus_1_frameshift	SO:0000282
0	"A transposable_element that is engineered and foreign." [SO:xp]	\N	engineered_foreign_transposable_element_gene	\N	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	42485	SO:0000283	\N	engineered_foreign_transposable_element_gene	SO:0000283
0	"A gene that is foreign." [SO:xp]	\N	foreign_gene	\N	\N	sequence	"A gene that is foreign." [SO:xp]	SO	42486	SO:0000285	\N	foreign_gene	SO:0000285
0	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42487	SO:0000286	\N	long_terminal_repeat	SO:0000286
0	"A gene that is a fusion." [SO:xp]	\N	fusion_gene	\N	\N	sequence	"A gene that is a fusion." [SO:xp]	SO	42488	SO:0000287	\N	fusion_gene	SO:0000287
0	"A fusion gene that is engineered." [SO:xp]	\N	engineered_fusion_gene	\N	\N	sequence	"A fusion gene that is engineered." [SO:xp]	SO	42489	SO:0000288	\N	engineered_fusion_gene	SO:0000288
0	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	SOFA	microsatellite	SOFA	\N	sequence	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	SO	42490	SO:0000289	\N	microsatellite	SO:0000289
0	"" []	\N	dinucleotide_repeat_microsatellite_feature	\N	\N	sequence	"" []	SO	42491	SO:0000290	\N	dinucleotide_repeat_microsatellite_feature	SO:0000290
0	"" []	\N	trinucleotide_repeat_microsatellite_feature	\N	\N	sequence	"" []	SO	42492	SO:0000291	\N	trinucleotide_repeat_microsatellite_feature	SO:0000291
0	"A repetitive element that is engineered and foreign." [SO:xp]	\N	engineered_foreign_repetitive_element	\N	\N	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	42493	SO:0000293	\N	engineered_foreign_repetitive_element	SO:0000293
0	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	SOFA	inverted_repeat	SOFA	\N	sequence	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	SO	42494	SO:0000294	\N	inverted_repeat	SO:0000294
0	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	\N	U12_intron	\N	\N	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	42495	SO:0000295	\N	U12_intron	SO:0000295
0	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	origin_of_replication	SOFA	\N	sequence	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42496	SO:0000296	\N	origin_of_replication	SO:0000296
0	"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	D_loop	\N	\N	sequence	"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42497	SO:0000297	\N	D_loop	SO:0000297
0	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	42498	SO:0000298	\N	recombination_feature	SO:0000298
0	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	42499	SO:0000299	\N	specific_recombination_site	SO:0000299
0	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	42500	SO:0000300	\N	recombination_feature_of_rearranged_gene	SO:0000300
0	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	42501	SO:0000301	\N	vertebrate_immune_system_gene_recombination_feature	SO:0000301
0	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_gene_recombination_feature	\N	\N	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42502	SO:0000302	\N	J_gene_recombination_feature	SO:0000302
0	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SOFA	clip	SOFA	\N	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	42503	SO:0000303	\N	clip	SO:0000303
0	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	modified_DNA_base	SOFA	\N	sequence	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42504	SO:0000305	\N	modified_DNA_base	SO:0000305
0	"A nucleotide modified by methylation." [SO:ke]	SOFA	methylated_DNA_base_feature	SOFA	\N	sequence	"A nucleotide modified by methylation." [SO:ke]	SO	42505	SO:0000306	\N	methylated_DNA_base_feature	SO:0000306
0	"Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]	SOFA	CpG_island	SOFA	\N	sequence	"Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]	SO	42506	SO:0000307	\N	CpG_island	SO:0000307
0	"Attribute to describe a feature that has been experimentally verified." [SO:ke]	\N	experimentally_determined	\N	\N	sequence	"Attribute to describe a feature that has been experimentally verified." [SO:ke]	SO	42507	SO:0000312	\N	experimentally_determined	SO:0000312
0	"A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	stem_loop	\N	\N	sequence	"A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42508	SO:0000313	\N	stem_loop	SO:0000313
0	"A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]	SOFA	direct_repeat	SOFA	\N	sequence	"A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]	SO	42509	SO:0000314	\N	direct_repeat	SO:0000314
0	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SOFA	TSS	SOFA	\N	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	42510	SO:0000315	\N	TSS	SO:0000315
0	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SOFA	CDS	SOFA	\N	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	42511	SO:0000316	\N	CDS	SO:0000316
0	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	\N	cDNA_clone	\N	\N	sequence	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	42512	SO:0000317	\N	cDNA_clone	SO:0000317
0	"First codon to be translated by a ribosome." [SO:ke]	SOFA	start_codon	SOFA	\N	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	42513	SO:0000318	\N	start_codon	SO:0000318
0	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SOFA	stop_codon	SOFA	\N	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	42514	SO:0000319	\N	stop_codon	SO:0000319
0	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	\N	intronic_splice_enhancer	\N	\N	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	42515	SO:0000320	\N	intronic_splice_enhancer	SO:0000320
0	"An mRNA with a plus 1 frameshift." [SO:ke]	\N	mRNA_with_plus_1_frameshift	\N	\N	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	42516	SO:0000321	\N	mRNA_with_plus_1_frameshift	SO:0000321
0	"" []	\N	nuclease_hypersensitive_site	\N	\N	sequence	"" []	SO	42517	SO:0000322	\N	nuclease_hypersensitive_site	SO:0000322
0	"The first base to be translated into protein." [SO:ke]	\N	coding_start	\N	\N	sequence	"The first base to be translated into protein." [SO:ke]	SO	42518	SO:0000323	\N	coding_start	SO:0000323
0	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SOFA	tag	SOFA	\N	sequence	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SO	42519	SO:0000324	\N	tag	SO:0000324
0	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SOFA	rRNA_large_subunit_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	42520	SO:0000325	\N	rRNA_large_subunit_primary_transcript	SO:0000325
0	"A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	SOFA	SAGE_tag	SOFA	\N	sequence	"A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	SO	42521	SO:0000326	\N	SAGE_tag	SO:0000326
0	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	\N	coding_end	\N	\N	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	42522	SO:0000327	\N	coding_end	SO:0000327
0	"" []	\N	microarray_oligo	\N	\N	sequence	"" []	SO	42523	SO:0000328	\N	microarray_oligo	SO:0000328
0	"An mRNA with a plus 2 frameshift." [SO:xp]	\N	mRNA_with_plus_2_frameshift	\N	\N	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	42524	SO:0000329	\N	mRNA_with_plus_2_frameshift	SO:0000329
0	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	SOFA	conserved_region	SOFA	\N	sequence	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	42525	SO:0000330	\N	conserved_region	SO:0000330
0	"Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]	SOFA	STS	SOFA	\N	sequence	"Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]	SO	42526	SO:0000331	\N	STS	SO:0000331
0	"Coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SOFA	coding_conserved_region	SOFA	\N	sequence	"Coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	42527	SO:0000332	\N	coding_conserved_region	SO:0000332
0	"The boundary between two exons in a processed transcript." [SO:ke]	SOFA	exon_junction	SOFA	\N	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	42528	SO:0000333	\N	exon_junction	SO:0000333
0	"Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SOFA	nc_conserved_region	SOFA	\N	sequence	"Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	42529	SO:0000334	\N	nc_conserved_region	SO:0000334
0	"A mRNA with a minus 2 frameshift." [SO:ke]	\N	mRNA_with_minus_2_frameshift	\N	\N	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	42530	SO:0000335	\N	mRNA_with_minus_2_frameshift	SO:0000335
0	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SOFA	pseudogene	SOFA	\N	sequence	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	42531	SO:0000336	\N	pseudogene	SO:0000336
0	"A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]	SOFA	RNAi_reagent	SOFA	\N	sequence	"A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]	SO	42532	SO:0000337	\N	RNAi_reagent	SO:0000337
0	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	\N	MITE	\N	\N	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	42533	SO:0000338	\N	MITE	SO:0000338
0	"A region in a genome which promotes recombination." [SO:rd]	\N	recombination_hotspot	\N	\N	sequence	"A region in a genome which promotes recombination." [SO:rd]	SO	42534	SO:0000339	\N	recombination_hotspot	SO:0000339
0	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SOFA	chromosome	SOFA	\N	sequence	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SO	42535	SO:0000340	\N	chromosome	SO:0000340
0	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SOFA	chromosome_band	SOFA	\N	sequence	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SO	42536	SO:0000341	\N	chromosome_band	SO:0000341
0	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"" []	SO	42537	SO:0000342	\N	site_specific_recombination_target_region	SO:0000342
0	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	\N	sequence	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SO	42538	SO:0000343	\N	match	SO:0000343
0	"Region of a transcript that regulates splicing." [SO:ke]	SOFA	splice_enhancer	SOFA	\N	sequence	"Region of a transcript that regulates splicing." [SO:ke]	SO	42539	SO:0000344	\N	splice_enhancer	SO:0000344
0	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	SOFA	EST	SOFA	\N	sequence	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	SO	42540	SO:0000345	\N	EST	SO:0000345
0	"" []	\N	loxP_site	\N	\N	sequence	"" []	SO	42541	SO:0000346	\N	loxP_site	SO:0000346
0	"A match against a nucleotide sequence." [SO:ke]	SOFA	nucleotide_match	SOFA	\N	sequence	"A match against a nucleotide sequence." [SO:ke]	SO	42542	SO:0000347	\N	nucleotide_match	SO:0000347
0	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	SO	42543	SO:0000348	\N	nucleic_acid	SO:0000348
0	"A match against a protein sequence." [SO:ke]	SOFA	protein_match	SOFA	\N	sequence	"A match against a protein sequence." [SO:ke]	SO	42544	SO:0000349	\N	protein_match	SO:0000349
0	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	\N	FRT_site	\N	\N	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	42545	SO:0000350	\N	FRT_site	SO:0000350
0	"An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]	\N	synthetic_sequence	\N	\N	sequence	"An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]	SO	42546	SO:0000351	\N	synthetic_sequence	SO:0000351
0	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	\N	DNA	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	SO	42547	SO:0000352	\N	DNA	SO:0000352
0	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	\N	sequence	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SO	42548	SO:0000353	\N	sequence_assembly	SO:0000353
0	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	\N	group_1_intron_homing_endonuclease_target_region	\N	\N	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	42549	SO:0000354	\N	group_1_intron_homing_endonuclease_target_region	SO:0000354
0	"A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]	\N	haplotype_block	\N	\N	sequence	"A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]	SO	42550	SO:0000355	\N	haplotype_block	SO:0000355
0	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb]	\N	RNA	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb]	SO	42551	SO:0000356	\N	RNA	SO:0000356
0	"An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]	\N	flanked	\N	\N	sequence	"An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]	SO	42552	SO:0000357	\N	flanked	SO:0000357
0	"An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]	\N	floxed	\N	\N	sequence	"An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]	SO	42553	SO:0000359	\N	floxed	SO:0000359
0	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SOFA	codon	SOFA	\N	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	42554	SO:0000360	\N	codon	SO:0000360
0	"An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]	\N	FRT_flanked	\N	\N	sequence	"An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]	SO	42555	SO:0000361	\N	FRT_flanked	SO:0000361
0	"A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]	\N	invalidated_by_chimeric_cDNA	\N	\N	sequence	"A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]	SO	42556	SO:0000362	\N	invalidated_by_chimeric_cDNA	SO:0000362
0	"A transgene that is floxed." [SO:xp]	\N	floxed_gene	\N	\N	sequence	"A transgene that is floxed." [SO:xp]	SO	42557	SO:0000363	\N	floxed_gene	SO:0000363
0	"The region of sequence surrounding a transposable element." [SO:ke]	\N	transposable_element_flanking_region	\N	\N	sequence	"The region of sequence surrounding a transposable element." [SO:ke]	SO	42558	SO:0000364	\N	transposable_element_flanking_region	SO:0000364
0	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	\N	integron	\N	\N	sequence	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	SO	42559	SO:0000365	\N	integron	SO:0000365
0	"The junction where an insertion occurred." [SO:ke]	SOFA	insertion_site	SOFA	\N	sequence	"The junction where an insertion occurred." [SO:ke]	SO	42560	SO:0000366	\N	insertion_site	SO:0000366
0	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	\N	attI_site	\N	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	42561	SO:0000367	\N	attI_site	SO:0000367
0	"The junction in a genome where a transposable_element has inserted." [SO:ke]	SOFA	transposable_element_insertion_site	SOFA	\N	sequence	"The junction in a genome where a transposable_element has inserted." [SO:ke]	SO	42562	SO:0000368	\N	transposable_element_insertion_site	SO:0000368
0	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SOFA	small_regulatory_ncRNA	SOFA	\N	sequence	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SO	42563	SO:0000370	\N	small_regulatory_ncRNA	SO:0000370
0	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	\N	conjugative_transposon	\N	\N	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	42564	SO:0000371	\N	conjugative_transposon	SO:0000371
0	"An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SOFA	enzymatic_RNA	SOFA	\N	sequence	"An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	42565	SO:0000372	\N	enzymatic_RNA	SO:0000372
0	"A recombinationally rearranged gene by inversion." [SO:xp]	\N	recombinationally_inverted_gene	\N	\N	sequence	"A recombinationally rearranged gene by inversion." [SO:xp]	SO	42566	SO:0000373	\N	recombinationally_inverted_gene	SO:0000373
0	"An RNA with catalytic activity." [SO:ma]	SOFA	ribozyme	SOFA	\N	sequence	"An RNA with catalytic activity." [SO:ma]	SO	42567	SO:0000374	\N	ribozyme	SO:0000374
0	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SOFA	rRNA_5_8S	SOFA	\N	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	42568	SO:0000375	\N	rRNA_5_8S	SO:0000375
0	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	\N	RNA_6S	\N	\N	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	42569	SO:0000376	\N	RNA_6S	SO:0000376
0	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	\N	CsrB_RsmB_RNA	\N	\N	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	42570	SO:0000377	\N	CsrB_RsmB_RNA	SO:0000377
0	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	\N	DsrA_RNA	\N	\N	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	42571	SO:0000378	\N	DsrA_RNA	SO:0000378
0	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	\N	GcvB_RNA	\N	\N	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	42572	SO:0000379	\N	GcvB_RNA	SO:0000379
0	"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]	SOFA	hammerhead_ribozyme	SOFA	\N	sequence	"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]	SO	42573	SO:0000380	\N	hammerhead_ribozyme	SO:0000380
0	"" []	\N	group_IIA_intron	\N	\N	sequence	"" []	SO	42574	SO:0000381	\N	group_IIA_intron	SO:0000381
0	"" []	\N	group_IIB_intron	\N	\N	sequence	"" []	SO	42575	SO:0000382	\N	group_IIB_intron	SO:0000382
0	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	\N	MicF_RNA	\N	\N	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	42576	SO:0000383	\N	MicF_RNA	SO:0000383
0	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	\N	OxyS_RNA	\N	\N	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	42577	SO:0000384	\N	OxyS_RNA	SO:0000384
0	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SOFA	RNase_MRP_RNA	SOFA	\N	sequence	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SO	42578	SO:0000385	\N	RNase_MRP_RNA	SO:0000385
0	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SOFA	RNase_P_RNA	SOFA	\N	sequence	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SO	42579	SO:0000386	\N	RNase_P_RNA	SO:0000386
0	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	\N	RprA_RNA	\N	\N	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	42580	SO:0000387	\N	RprA_RNA	SO:0000387
0	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	\N	RRE_RNA	\N	\N	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	42581	SO:0000388	\N	RRE_RNA	SO:0000388
0	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	\N	spot_42_RNA	\N	\N	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	42582	SO:0000389	\N	spot_42_RNA	SO:0000389
0	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SOFA	telomerase_RNA	SOFA	\N	sequence	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SO	42583	SO:0000390	\N	telomerase_RNA	SO:0000390
0	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SOFA	U1_snRNA	SOFA	\N	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	42584	SO:0000391	\N	U1_snRNA	SO:0000391
0	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SOFA	U2_snRNA	SOFA	\N	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	42585	SO:0000392	\N	U2_snRNA	SO:0000392
0	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SOFA	U4_snRNA	SOFA	\N	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	42586	SO:0000393	\N	U4_snRNA	SO:0000393
0	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SOFA	U4atac_snRNA	SOFA	\N	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	42587	SO:0000394	\N	U4atac_snRNA	SO:0000394
0	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SOFA	U5_snRNA	SOFA	\N	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	42588	SO:0000395	\N	U5_snRNA	SO:0000395
0	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SOFA	U6_snRNA	SOFA	\N	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	42589	SO:0000396	\N	U6_snRNA	SO:0000396
0	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SOFA	U6atac_snRNA	SOFA	\N	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	42590	SO:0000397	\N	U6atac_snRNA	SO:0000397
0	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SOFA	U11_snRNA	SOFA	\N	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	42591	SO:0000398	\N	U11_snRNA	SO:0000398
0	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SOFA	U12_snRNA	SOFA	\N	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	42592	SO:0000399	\N	U12_snRNA	SO:0000399
0	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describes a quality of sequence." [SO:ke]	SO	42593	SO:0000400	\N	sequence_attribute	SO:0000400
0	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	42594	SO:0000401	\N	gene_attribute	SO:0000401
0	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SOFA	U14_snoRNA	SOFA	\N	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	42595	SO:0000403	\N	U14_snoRNA	SO:0000403
0	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SOFA	vault_RNA	SOFA	\N	sequence	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SO	42596	SO:0000404	\N	vault_RNA	SO:0000404
0	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SOFA	Y_RNA	SOFA	\N	sequence	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SO	42597	SO:0000405	\N	Y_RNA	SO:0000405
0	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	\N	twintron	\N	\N	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	42598	SO:0000406	\N	twintron	SO:0000406
0	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SOFA	rRNA_18S	SOFA	\N	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	42599	SO:0000407	\N	rRNA_18S	SO:0000407
0	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens,SOFA	binding_site	biosapiens,SOFA	\N	sequence	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SO	42600	SO:0000409	\N	binding_site	SO:0000409
0	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SOFA	protein_binding_site	SOFA	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SO	42601	SO:0000410	\N	protein_binding_site	SO:0000410
0	"A region that rescues." [SO:xp]	\N	rescue_region	\N	\N	sequence	"A region that rescues." [SO:xp]	SO	42602	SO:0000411	\N	rescue_region	SO:0000411
0	"A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]	SOFA	restriction_fragment	SOFA	\N	sequence	"A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]	SO	42603	SO:0000412	\N	restriction_fragment	SO:0000412
0	"A region where the sequence differs from that of a specified sequence." [SO:ke]	SOFA	sequence_difference	SOFA	\N	sequence	"A region where the sequence differs from that of a specified sequence." [SO:ke]	SO	42604	SO:0000413	\N	sequence_difference	SO:0000413
0	"An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]	\N	invalidated_by_genomic_contamination	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]	SO	42605	SO:0000414	\N	invalidated_by_genomic_contamination	SO:0000414
0	"An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]	\N	invalidated_by_genomic_polyA_primed_cDNA	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]	SO	42606	SO:0000415	\N	invalidated_by_genomic_polyA_primed_cDNA	SO:0000415
0	"An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]	\N	invalidated_by_partial_processing	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]	SO	42607	SO:0000416	\N	invalidated_by_partial_processing	SO:0000416
0	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	biosapiens	polypeptide_domain	biosapiens	\N	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	42608	SO:0000417	\N	polypeptide_domain	SO:0000417
0	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	biosapiens,SOFA	signal_peptide	biosapiens,SOFA	\N	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42609	SO:0000418	\N	signal_peptide	SO:0000418
0	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	biosapiens,SOFA	mature_protein_region	biosapiens,SOFA	\N	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	42610	SO:0000419	\N	mature_protein_region	SO:0000419
0	"" []	\N	five_prime_terminal_inverted_repeat	\N	\N	sequence	"" []	SO	42611	SO:0000420	\N	five_prime_terminal_inverted_repeat	SO:0000420
0	"" []	\N	three_prime_terminal_inverted_repeat	\N	\N	sequence	"" []	SO	42612	SO:0000421	\N	three_prime_terminal_inverted_repeat	SO:0000421
0	"" []	\N	U5_LTR_region	\N	\N	sequence	"" []	SO	42613	SO:0000422	\N	U5_LTR_region	SO:0000422
0	"" []	\N	R_LTR_region	\N	\N	sequence	"" []	SO	42614	SO:0000423	\N	R_LTR_region	SO:0000423
0	"" []	\N	U3_LTR_region	\N	\N	sequence	"" []	SO	42615	SO:0000424	\N	U3_LTR_region	SO:0000424
0	"" []	\N	five_prime_LTR	\N	\N	sequence	"" []	SO	42616	SO:0000425	\N	five_prime_LTR	SO:0000425
0	"" []	\N	three_prime_LTR	\N	\N	sequence	"" []	SO	42617	SO:0000426	\N	three_prime_LTR	SO:0000426
0	"" []	\N	R_five_prime_LTR_region	\N	\N	sequence	"" []	SO	42618	SO:0000427	\N	R_five_prime_LTR_region	SO:0000427
0	"" []	\N	U5_five_prime_LTR_region	\N	\N	sequence	"" []	SO	42619	SO:0000428	\N	U5_five_prime_LTR_region	SO:0000428
0	"" []	\N	U3_five_prime_LTR_region	\N	\N	sequence	"" []	SO	42620	SO:0000429	\N	U3_five_prime_LTR_region	SO:0000429
0	"" []	\N	R_three_prime_LTR_region	\N	\N	sequence	"" []	SO	42621	SO:0000430	\N	R_three_prime_LTR_region	SO:0000430
0	"" []	\N	U3_three_prime_LTR_region	\N	\N	sequence	"" []	SO	42622	SO:0000431	\N	U3_three_prime_LTR_region	SO:0000431
0	"" []	\N	U5_three_prime_LTR_region	\N	\N	sequence	"" []	SO	42623	SO:0000432	\N	U5_three_prime_LTR_region	SO:0000432
0	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	\N	non_LTR_retrotransposon_polymeric_tract	\N	\N	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	42624	SO:0000433	\N	non_LTR_retrotransposon_polymeric_tract	SO:0000433
0	"A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]	\N	target_site_duplication	\N	\N	sequence	"A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]	SO	42625	SO:0000434	\N	target_site_duplication	SO:0000434
0	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	\N	RR_tract	\N	\N	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	42626	SO:0000435	\N	RR_tract	SO:0000435
0	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	SOFA	ARS	SOFA	\N	sequence	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	SO	42627	SO:0000436	\N	ARS	SO:0000436
0	"" []	\N	inverted_ring_chromosome	\N	\N	sequence	"" []	SO	42628	SO:0000439	\N	inverted_ring_chromosome	SO:0000439
0	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	42629	SO:0000440	\N	vector_replicon	SO:0000440
0	"A single stranded oligonucleotide." [SO:ke]	SOFA	ss_oligo	SOFA	\N	sequence	"A single stranded oligonucleotide." [SO:ke]	SO	42630	SO:0000441	\N	ss_oligo	SO:0000441
0	"A double stranded oligonucleotide." [SO:ke]	SOFA	ds_oligo	SOFA	\N	sequence	"A double stranded oligonucleotide." [SO:ke]	SO	42631	SO:0000442	\N	ds_oligo	SO:0000442
0	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute to describe the kind of biological sequence." [SO:ke]	SO	42632	SO:0000443	\N	polymer_attribute	SO:0000443
0	"Non-coding exon in the 3' UTR." [SO:ke]	\N	three_prime_noncoding_exon	\N	\N	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	42633	SO:0000444	\N	three_prime_noncoding_exon	SO:0000444
0	"Non-coding exon in the 5' UTR." [SO:ke]	\N	five_prime_noncoding_exon	\N	\N	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	42634	SO:0000445	\N	five_prime_noncoding_exon	SO:0000445
0	"Intron located in the untranslated region." [SO:ke]	\N	UTR_intron	\N	\N	sequence	"Intron located in the untranslated region." [SO:ke]	SO	42635	SO:0000446	\N	UTR_intron	SO:0000446
0	"An intron located in the 5' UTR." [SO:ke]	\N	five_prime_UTR_intron	\N	\N	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	42636	SO:0000447	\N	five_prime_UTR_intron	SO:0000447
0	"An intron located in the 3' UTR." [SO:ke]	\N	three_prime_UTR_intron	\N	\N	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	42637	SO:0000448	\N	three_prime_UTR_intron	SO:0000448
0	"A sequence of nucleotides or amino acids which, by design, has a \\"random\\" order of components, given a predetermined input frequency of these components." [SO:ma]	\N	random_sequence	\N	\N	sequence	"A sequence of nucleotides or amino acids which, by design, has a \\"random\\" order of components, given a predetermined input frequency of these components." [SO:ma]	SO	42638	SO:0000449	\N	random_sequence	SO:0000449
0	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	\N	interband	\N	\N	sequence	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	SO	42639	SO:0000450	\N	interband	SO:0000450
0	"A gene that encodes a polyadenylated mRNA." [SO:xp]	\N	gene_with_polyadenylated_mRNA	\N	\N	sequence	"A gene that encodes a polyadenylated mRNA." [SO:xp]	SO	42640	SO:0000451	\N	gene_with_polyadenylated_mRNA	SO:0000451
0	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	42641	SO:0000453	\N	chromosomal_transposition	SO:0000453
0	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SOFA	rasiRNA	SOFA	\N	sequence	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SO	42642	SO:0000454	\N	rasiRNA	SO:0000454
0	"A gene that encodes an mRNA with a frameshift." [SO:xp]	\N	gene_with_mRNA_with_frameshift	\N	\N	sequence	"A gene that encodes an mRNA with a frameshift." [SO:xp]	SO	42643	SO:0000455	\N	gene_with_mRNA_with_frameshift	SO:0000455
0	"A gene that is recombinationally rearranged." [SO:ke]	\N	recombinationally_rearranged_gene	\N	\N	sequence	"A gene that is recombinationally rearranged." [SO:ke]	SO	42644	SO:0000456	\N	recombinationally_rearranged_gene	SO:0000456
0	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	\N	interchromosomal_duplication	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	42645	SO:0000457	\N	interchromosomal_duplication	SO:0000457
0	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	D_gene_segment	\N	\N	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42646	SO:0000458	\N	D_gene_segment	SO:0000458
0	"A gene with a transcript that is trans-spliced." [SO:xp]	\N	gene_with_trans_spliced_transcript	\N	\N	sequence	"A gene with a transcript that is trans-spliced." [SO:xp]	SO	42647	SO:0000459	\N	gene_with_trans_spliced_transcript	SO:0000459
0	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_segment	\N	\N	sequence	"" []	SO	42648	SO:0000460	\N	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000460
0	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	\N	inversion_derived_bipartite_deficiency	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	42649	SO:0000461	\N	inversion_derived_bipartite_deficiency	SO:0000461
0	"A non-functional descendant of a functional entity." [SO:cjm]	SOFA	pseudogenic_region	SOFA	\N	sequence	"A non-functional descendant of a functional entity." [SO:cjm]	SO	42650	SO:0000462	\N	pseudogenic_region	SO:0000462
0	"A gene that encodes more than one transcript." [SO:ke]	\N	encodes_alternately_spliced_transcripts	\N	\N	sequence	"A gene that encodes more than one transcript." [SO:ke]	SO	42651	SO:0000463	\N	encodes_alternately_spliced_transcripts	SO:0000463
0	"A non-functional descendant of an exon." [SO:ke]	SOFA	decayed_exon	SOFA	\N	sequence	"A non-functional descendant of an exon." [SO:ke]	SO	42652	SO:0000464	\N	decayed_exon	SO:0000464
0	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	\N	inversion_derived_deficiency_plus_duplication	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	42653	SO:0000465	\N	inversion_derived_deficiency_plus_duplication	SO:0000465
0	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_gene_segment	\N	\N	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42654	SO:0000466	\N	V_gene_segment	SO:0000466
0	"An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]	\N	post_translationally_regulated_by_protein_stability	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]	SO	42655	SO:0000467	\N	post_translationally_regulated_by_protein_stability	SO:0000467
0	"One of the pieces of sequence that make up a golden path." [SO:rd]	SOFA	golden_path_fragment	SOFA	\N	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	42656	SO:0000468	\N	golden_path_fragment	SO:0000468
0	"An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]	\N	post_translationally_regulated_by_protein_modification	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]	SO	42657	SO:0000469	\N	post_translationally_regulated_by_protein_modification	SO:0000469
0	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_gene_segment	\N	\N	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42658	SO:0000470	\N	J_gene_segment	SO:0000470
0	"The gene product is involved in its own transcriptional regulation." [SO:ke]	\N	autoregulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation." [SO:ke]	SO	42659	SO:0000471	\N	autoregulated	SO:0000471
0	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	SOFA	tiling_path	SOFA	\N	sequence	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	SO	42660	SO:0000472	\N	tiling_path	SO:0000472
0	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	\N	negatively_autoregulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	42661	SO:0000473	\N	negatively_autoregulated	SO:0000473
0	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SOFA	tiling_path_fragment	SOFA	\N	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	42662	SO:0000474	\N	tiling_path_fragment	SO:0000474
0	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	\N	positively_autoregulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	42663	SO:0000475	\N	positively_autoregulated	SO:0000475
0	"A DNA sequencer read which is part of a contig." [SO:ke]	\N	contig_read	\N	\N	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	42664	SO:0000476	\N	contig_read	SO:0000476
0	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	C_gene_segment	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42665	SO:0000478	\N	C_gene_segment	SO:0000478
0	"A transcript that is trans-spliced." [SO:xp]	\N	trans_spliced_transcript	\N	\N	sequence	"A transcript that is trans-spliced." [SO:xp]	SO	42666	SO:0000479	\N	trans_spliced_transcript	SO:0000479
0	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	\N	tiling_path_clone	\N	\N	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	42667	SO:0000480	\N	tiling_path_clone	SO:0000480
0	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	\N	terminal_inverted_repeat	\N	\N	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	42668	SO:0000481	\N	terminal_inverted_repeat	SO:0000481
0	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"" []	SO	42669	SO:0000482	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000482
0	"A primary transcript that is never translated into a protein." [SO:ke]	SOFA	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript that is never translated into a protein." [SO:ke]	SO	42670	SO:0000483	\N	nc_primary_transcript	SO:0000483
0	"The sequence of the 3' exon that is not coding." [SO:ke]	SOFA	three_prime_coding_exon_noncoding_region	SOFA	\N	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	42671	SO:0000484	\N	three_prime_coding_exon_noncoding_region	SO:0000484
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	DJ_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42672	SO:0000485	\N	DJ_J_cluster	SO:0000485
0	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SOFA	five_prime_coding_exon_noncoding_region	SOFA	\N	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	42673	SO:0000486	\N	five_prime_coding_exon_noncoding_region	SO:0000486
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VDJ_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42674	SO:0000487	\N	VDJ_J_C_cluster	SO:0000487
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VDJ_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42675	SO:0000488	\N	VDJ_J_cluster	SO:0000488
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VJ_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42676	SO:0000489	\N	VJ_C_cluster	SO:0000489
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VJ_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42677	SO:0000490	\N	VJ_J_C_cluster	SO:0000490
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VJ_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42678	SO:0000491	\N	VJ_J_cluster	SO:0000491
0	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"" []	SO	42679	SO:0000492	\N	D_gene_recombination_feature	SO:0000492
0	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	three_prime_D_heptamer	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42680	SO:0000493	\N	three_prime_D_heptamer	SO:0000493
0	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	three_prime_D_nonamer	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42681	SO:0000494	\N	three_prime_D_nonamer	SO:0000494
0	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	three_prime_D_spacer	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42682	SO:0000495	\N	three_prime_D_spacer	SO:0000495
0	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	five_prime_D_heptamer	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42683	SO:0000496	\N	five_prime_D_heptamer	SO:0000496
0	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	five_prime_D_nonamer	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42684	SO:0000497	\N	five_prime_D_nonamer	SO:0000497
0	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	five_prime_D_spacer	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42685	SO:0000498	\N	five_prime_D_spacer	SO:0000498
0	"A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]	SOFA	virtual_sequence	SOFA	\N	sequence	"A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]	SO	42686	SO:0000499	\N	virtual_sequence	SO:0000499
0	"A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]	\N	Hoogsteen_base_pair	\N	\N	sequence	"A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]	SO	42687	SO:0000500	\N	Hoogsteen_base_pair	SO:0000500
0	"A type of non-canonical base-pairing." [SO:ke]	\N	reverse_Hoogsteen_base_pair	\N	\N	sequence	"A type of non-canonical base-pairing." [SO:ke]	SO	42688	SO:0000501	\N	reverse_Hoogsteen_base_pair	SO:0000501
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	D_DJ_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42689	SO:0000504	\N	D_DJ_C_cluster	SO:0000504
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	D_DJ_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42690	SO:0000505	\N	D_DJ_cluster	SO:0000505
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	D_DJ_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42691	SO:0000506	\N	D_DJ_J_C_cluster	SO:0000506
0	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	\N	pseudogenic_exon	\N	\N	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	42692	SO:0000507	\N	pseudogenic_exon	SO:0000507
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	D_DJ_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42693	SO:0000508	\N	D_DJ_J_cluster	SO:0000508
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	D_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42694	SO:0000509	\N	D_J_C_cluster	SO:0000509
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VD_gene_segment	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42695	SO:0000510	\N	VD_gene_segment	SO:0000510
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42696	SO:0000511	\N	J_C_cluster	SO:0000511
0	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	\N	inversion_derived_deficiency_plus_aneuploid	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	42697	SO:0000512	\N	inversion_derived_deficiency_plus_aneuploid	SO:0000512
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42698	SO:0000513	\N	J_cluster	SO:0000513
0	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_nonamer	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42699	SO:0000514	\N	J_nonamer	SO:0000514
0	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_heptamer	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42700	SO:0000515	\N	J_heptamer	SO:0000515
0	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	\N	pseudogenic_transcript	\N	\N	sequence	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	SO	42701	SO:0000516	\N	pseudogenic_transcript	SO:0000516
0	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_spacer	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42702	SO:0000517	\N	J_spacer	SO:0000517
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_DJ_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42703	SO:0000518	\N	V_DJ_cluster	SO:0000518
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_DJ_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42704	SO:0000519	\N	V_DJ_J_cluster	SO:0000519
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_VDJ_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42705	SO:0000520	\N	V_VDJ_C_cluster	SO:0000520
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_VDJ_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42706	SO:0000521	\N	V_VDJ_cluster	SO:0000521
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_VDJ_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42707	SO:0000522	\N	V_VDJ_J_cluster	SO:0000522
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_VJ_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42708	SO:0000523	\N	V_VJ_C_cluster	SO:0000523
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_VJ_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42709	SO:0000524	\N	V_VJ_cluster	SO:0000524
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_VJ_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42710	SO:0000525	\N	V_VJ_J_cluster	SO:0000525
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42711	SO:0000526	\N	V_cluster	SO:0000526
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_D_DJ_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42712	SO:0000527	\N	V_D_DJ_C_cluster	SO:0000527
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_D_DJ_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42713	SO:0000528	\N	V_D_DJ_cluster	SO:0000528
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_D_DJ_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42714	SO:0000529	\N	V_D_DJ_J_C_cluster	SO:0000529
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_D_DJ_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42715	SO:0000530	\N	V_D_DJ_J_cluster	SO:0000530
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_D_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42716	SO:0000531	\N	V_D_J_C_cluster	SO:0000531
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_D_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42717	SO:0000532	\N	V_D_J_cluster	SO:0000532
0	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_heptamer	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42718	SO:0000533	\N	V_heptamer	SO:0000533
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42719	SO:0000534	\N	V_J_cluster	SO:0000534
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42720	SO:0000535	\N	V_J_C_cluster	SO:0000535
0	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_nonamer	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42721	SO:0000536	\N	V_nonamer	SO:0000536
0	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_spacer	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42722	SO:0000537	\N	V_spacer	SO:0000537
0	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_gene_recombination_feature	\N	\N	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42723	SO:0000538	\N	V_gene_recombination_feature	SO:0000538
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	DJ_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42724	SO:0000539	\N	DJ_C_cluster	SO:0000539
0	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	DJ_J_C_cluster	\N	\N	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42725	SO:0000540	\N	DJ_J_C_cluster	SO:0000540
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VDJ_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42726	SO:0000541	\N	VDJ_C_cluster	SO:0000541
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_DJ_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42727	SO:0000542	\N	V_DJ_C_cluster	SO:0000542
0	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	\N	helitron	\N	\N	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	42728	SO:0000544	\N	helitron	SO:0000544
0	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	\N	recoding_pseudoknot	\N	\N	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	42729	SO:0000545	\N	recoding_pseudoknot	SO:0000545
0	"" []	\N	designed_sequence	\N	\N	sequence	"" []	SO	42730	SO:0000546	\N	designed_sequence	SO:0000546
0	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	\N	inversion_derived_bipartite_duplication	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	42731	SO:0000547	\N	inversion_derived_bipartite_duplication	SO:0000547
0	"A gene that encodes a transcript that is edited." [SO:xp]	\N	gene_with_edited_transcript	\N	\N	sequence	"A gene that encodes a transcript that is edited." [SO:xp]	SO	42732	SO:0000548	\N	gene_with_edited_transcript	SO:0000548
0	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	\N	inversion_derived_duplication_plus_aneuploid	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	42733	SO:0000549	\N	inversion_derived_duplication_plus_aneuploid	SO:0000549
0	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	\N	aneuploid_chromosome	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	42734	SO:0000550	\N	aneuploid_chromosome	SO:0000550
0	"The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	polyA_signal_sequence	SOFA	\N	sequence	"The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42735	SO:0000551	\N	polyA_signal_sequence	SO:0000551
0	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	\N	Shine_Dalgarno_sequence	\N	\N	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	42736	SO:0000552	\N	Shine_Dalgarno_sequence	SO:0000552
0	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	polyA_site	SOFA	\N	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42737	SO:0000553	\N	polyA_site	SO:0000553
0	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	five_prime_clip	\N	\N	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42738	SO:0000555	\N	five_prime_clip	SO:0000555
0	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	five_prime_D_recombination_signal_sequence	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42739	SO:0000556	\N	five_prime_D_recombination_signal_sequence	SO:0000556
0	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	three_prime_clip	\N	\N	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42740	SO:0000557	\N	three_prime_clip	SO:0000557
0	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42741	SO:0000558	\N	C_cluster	SO:0000558
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	D_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42742	SO:0000559	\N	D_cluster	SO:0000559
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	D_J_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42743	SO:0000560	\N	D_J_cluster	SO:0000560
0	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42744	SO:0000561	\N	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000561
0	"" []	\N	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"" []	SO	42745	SO:0000562	\N	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000562
0	"" []	\N	vertebrate_immune_system_gene_recombination_spacer	\N	\N	sequence	"" []	SO	42746	SO:0000563	\N	vertebrate_immune_system_gene_recombination_spacer	SO:0000563
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_DJ_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42747	SO:0000564	\N	V_DJ_J_C_cluster	SO:0000564
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_VDJ_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42748	SO:0000565	\N	V_VDJ_J_C_cluster	SO:0000565
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_VJ_J_C_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42749	SO:0000566	\N	V_VJ_J_C_cluster	SO:0000566
0	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	\N	inversion_derived_aneuploid_chromosome	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	42750	SO:0000567	\N	inversion_derived_aneuploid_chromosome	SO:0000567
0	"" []	\N	bidirectional_promoter	\N	\N	sequence	"" []	SO	42751	SO:0000568	\N	bidirectional_promoter	SO:0000568
0	"An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke]	\N	retrotransposed	\N	\N	sequence	"An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke]	SO	42752	SO:0000569	\N	retrotransposed	SO:0000569
0	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	three_prime_D_recombination_signal_sequence	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42753	SO:0000570	\N	three_prime_D_recombination_signal_sequence	SO:0000570
0	"" []	\N	miRNA_encoding	\N	\N	sequence	"" []	SO	42754	SO:0000571	\N	miRNA_encoding	SO:0000571
0	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	DJ_gene_segment	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42755	SO:0000572	\N	DJ_gene_segment	SO:0000572
0	"" []	\N	rRNA_encoding	\N	\N	sequence	"" []	SO	42756	SO:0000573	\N	rRNA_encoding	SO:0000573
0	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VDJ_gene_segment	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42757	SO:0000574	\N	VDJ_gene_segment	SO:0000574
0	"" []	\N	scRNA_encoding	\N	\N	sequence	"" []	SO	42758	SO:0000575	\N	scRNA_encoding	SO:0000575
0	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	VJ_gene_segment	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	42759	SO:0000576	\N	VJ_gene_segment	SO:0000576
0	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SOFA	centromere	SOFA	\N	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	42760	SO:0000577	\N	centromere	SO:0000577
0	"" []	\N	snoRNA_encoding	\N	\N	sequence	"" []	SO	42761	SO:0000578	\N	snoRNA_encoding	SO:0000578
0	"A locatable feature on a transcript that is edited." [SO:ma]	\N	edited_transcript_feature	\N	\N	sequence	"A locatable feature on a transcript that is edited." [SO:ma]	SO	42762	SO:0000579	\N	edited_transcript_feature	SO:0000579
0	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	\N	methylation_guide_snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	42763	SO:0000580	\N	methylation_guide_snoRNA_primary_transcript	SO:0000580
0	"A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SOFA	cap	SOFA	\N	sequence	"A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	42764	SO:0000581	\N	cap	SO:0000581
0	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	\N	rRNA_cleavage_snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	42765	SO:0000582	\N	rRNA_cleavage_snoRNA_primary_transcript	SO:0000582
0	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	\N	pre_edited_region	\N	\N	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	42766	SO:0000583	\N	pre_edited_region	SO:0000583
0	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	\N	tmRNA	\N	\N	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	42767	SO:0000584	\N	tmRNA	SO:0000584
0	"" []	\N	C_D_box_snoRNA_encoding	\N	\N	sequence	"" []	SO	42768	SO:0000585	\N	C_D_box_snoRNA_encoding	SO:0000585
0	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	\N	tmRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	SO	42769	SO:0000586	\N	tmRNA_primary_transcript	SO:0000586
0	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SOFA	group_I_intron	SOFA	\N	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	42770	SO:0000587	\N	group_I_intron	SO:0000587
0	"A self spliced intron." [SO:ke]	SOFA	autocatalytically_spliced_intron	SOFA	\N	sequence	"A self spliced intron." [SO:ke]	SO	42771	SO:0000588	\N	autocatalytically_spliced_intron	SO:0000588
0	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	\N	SRP_RNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	SO	42772	SO:0000589	\N	SRP_RNA_primary_transcript	SO:0000589
0	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SOFA	SRP_RNA	SOFA	\N	sequence	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SO	42773	SO:0000590	\N	SRP_RNA	SO:0000590
0	"A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]	\N	pseudoknot	\N	\N	sequence	"A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]	SO	42774	SO:0000591	\N	pseudoknot	SO:0000591
0	"A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]	\N	H_pseudoknot	\N	\N	sequence	"A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]	SO	42775	SO:0000592	\N	H_pseudoknot	SO:0000592
0	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SOFA	C_D_box_snoRNA	SOFA	\N	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	42776	SO:0000593	\N	C_D_box_snoRNA	SO:0000593
0	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	\N	H_ACA_box_snoRNA	\N	\N	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	42777	SO:0000594	\N	H_ACA_box_snoRNA	SO:0000594
0	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	\N	C_D_box_snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	42778	SO:0000595	\N	C_D_box_snoRNA_primary_transcript	SO:0000595
0	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	\N	H_ACA_box_snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	42779	SO:0000596	\N	H_ACA_box_snoRNA_primary_transcript	SO:0000596
0	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SOFA	guide_RNA	SOFA	\N	sequence	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SO	42780	SO:0000602	\N	guide_RNA	SO:0000602
0	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SOFA	group_II_intron	SOFA	\N	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	42781	SO:0000603	\N	group_II_intron	SO:0000603
0	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	\N	editing_block	\N	\N	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	42782	SO:0000604	\N	editing_block	SO:0000604
0	"A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]	SOFA	intergenic_region	SOFA	\N	sequence	"A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]	SO	42783	SO:0000605	\N	intergenic_region	SO:0000605
0	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	\N	editing_domain	\N	\N	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	42784	SO:0000606	\N	editing_domain	SO:0000606
0	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	\N	unedited_region	\N	\N	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	42785	SO:0000607	\N	unedited_region	SO:0000607
0	"" []	\N	H_ACA_box_snoRNA_encoding	\N	\N	sequence	"" []	SO	42786	SO:0000608	\N	H_ACA_box_snoRNA_encoding	SO:0000608
0	"The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]	\N	oligo_U_tail	\N	\N	sequence	"The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]	SO	42787	SO:0000609	\N	oligo_U_tail	SO:0000609
0	"Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]	SOFA	polyA_sequence	SOFA	\N	sequence	"Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]	SO	42788	SO:0000610	\N	polyA_sequence	SO:0000610
0	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SOFA	branch_site	SOFA	\N	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	42789	SO:0000611	\N	branch_site	SO:0000611
0	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SOFA	polypyrimidine_tract	SOFA	\N	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	42790	SO:0000612	\N	polypyrimidine_tract	SO:0000612
0	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	42791	SO:0000613	\N	bacterial_RNApol_promoter	SO:0000613
0	"A terminator signal for bacterial transcription." [SO:ke]	\N	bacterial_terminator	\N	\N	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	42792	SO:0000614	\N	bacterial_terminator	SO:0000614
0	"A terminator signal for RNA polymerase III transcription." [SO:ke]	\N	terminator_of_type_2_RNApol_III_promoter	\N	\N	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	42793	SO:0000615	\N	terminator_of_type_2_RNApol_III_promoter	SO:0000615
0	"The base where transcription ends." [SO:ke]	SOFA	transcription_end_site	SOFA	\N	sequence	"The base where transcription ends." [SO:ke]	SO	42794	SO:0000616	\N	transcription_end_site	SO:0000616
0	"" []	\N	RNApol_III_promoter_type_1	\N	\N	sequence	"" []	SO	42795	SO:0000617	\N	RNApol_III_promoter_type_1	SO:0000617
0	"" []	\N	RNApol_III_promoter_type_2	\N	\N	sequence	"" []	SO	42796	SO:0000618	\N	RNApol_III_promoter_type_2	SO:0000618
0	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	\N	A_box	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	42797	SO:0000619	\N	A_box	SO:0000619
0	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	\N	B_box	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	42798	SO:0000620	\N	B_box	SO:0000620
0	"" []	\N	RNApol_III_promoter_type_3	\N	\N	sequence	"" []	SO	42799	SO:0000621	\N	RNApol_III_promoter_type_3	SO:0000621
0	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	\N	C_box	\N	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	42800	SO:0000622	\N	C_box	SO:0000622
0	"" []	\N	snRNA_encoding	\N	\N	sequence	"" []	SO	42801	SO:0000623	\N	snRNA_encoding	SO:0000623
0	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SOFA	telomere	SOFA	\N	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	42802	SO:0000624	\N	telomere	SO:0000624
0	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SOFA	silencer	SOFA	\N	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	42803	SO:0000625	\N	silencer	SO:0000625
0	"" []	\N	chromosomal_regulatory_element	\N	\N	sequence	"" []	SO	42804	SO:0000626	\N	chromosomal_regulatory_element	SO:0000626
0	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SOFA	insulator	SOFA	\N	sequence	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SO	42805	SO:0000627	\N	insulator	SO:0000627
0	"" []	SOFA	chromosomal_structural_element	SOFA	\N	sequence	"" []	SO	42806	SO:0000628	\N	chromosomal_structural_element	SO:0000628
0	"" []	\N	five_prime_open_reading_frame	\N	\N	sequence	"" []	SO	42807	SO:0000629	\N	five_prime_open_reading_frame	SO:0000629
0	"A start codon upstream of the ORF." [SO:ke]	\N	upstream_AUG_codon	\N	\N	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	42808	SO:0000630	\N	upstream_AUG_codon	SO:0000630
0	"A primary transcript encoding for more than one gene product." [SO:ke]	\N	polycistronic_primary_transcript	\N	\N	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	42809	SO:0000631	\N	polycistronic_primary_transcript	SO:0000631
0	"A primary transcript encoding for one gene product." [SO:ke]	\N	monocistronic_primary_transcript	\N	\N	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	42810	SO:0000632	\N	monocistronic_primary_transcript	SO:0000632
0	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	\N	monocistronic_mRNA	\N	\N	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	42811	SO:0000633	\N	monocistronic_mRNA	SO:0000633
0	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	\N	polycistronic_mRNA	\N	\N	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	42812	SO:0000634	\N	polycistronic_mRNA	SO:0000634
0	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	\N	mini_exon_donor_RNA	\N	\N	sequence	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	SO	42813	SO:0000635	\N	mini_exon_donor_RNA	SO:0000635
0	"" []	\N	spliced_leader_RNA	\N	\N	sequence	"" []	SO	42814	SO:0000636	\N	spliced_leader_RNA	SO:0000636
0	"A plasmid that is engineered." [SO:xp]	\N	engineered_plasmid	\N	\N	sequence	"A plasmid that is engineered." [SO:xp]	SO	42815	SO:0000637	\N	engineered_plasmid	SO:0000637
0	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	\N	transcribed_spacer_region	\N	\N	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	42816	SO:0000638	\N	transcribed_spacer_region	SO:0000638
0	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	\N	internal_transcribed_spacer_region	\N	\N	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	42817	SO:0000639	\N	internal_transcribed_spacer_region	SO:0000639
0	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	\N	external_transcribed_spacer_region	\N	\N	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	42818	SO:0000640	\N	external_transcribed_spacer_region	SO:0000640
0	"" []	\N	tetranucleotide_repeat_microsatellite_feature	\N	\N	sequence	"" []	SO	42819	SO:0000641	\N	tetranucleotide_repeat_microsatellite_feature	SO:0000641
0	"" []	\N	SRP_RNA_encoding	\N	\N	sequence	"" []	SO	42820	SO:0000642	\N	SRP_RNA_encoding	SO:0000642
0	"A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]	SOFA	minisatellite	SOFA	\N	sequence	"A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]	SO	42821	SO:0000643	\N	minisatellite	SO:0000643
0	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SOFA	antisense_RNA	SOFA	\N	sequence	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SO	42822	SO:0000644	\N	antisense_RNA	SO:0000644
0	"The reverse complement of the primary transcript." [SO:ke]	SOFA	antisense_primary_transcript	SOFA	\N	sequence	"The reverse complement of the primary transcript." [SO:ke]	SO	42823	SO:0000645	\N	antisense_primary_transcript	SO:0000645
0	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SOFA	siRNA	SOFA	\N	sequence	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SO	42824	SO:0000646	\N	siRNA	SO:0000646
0	"A primary transcript encoding a micro RNA." [SO:ke]	\N	miRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a micro RNA." [SO:ke]	SO	42825	SO:0000647	\N	miRNA_primary_transcript	SO:0000647
0	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	\N	stRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	42826	SO:0000648	\N	stRNA_primary_transcript	SO:0000648
0	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SOFA	stRNA	SOFA	\N	sequence	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SO	42827	SO:0000649	\N	stRNA	SO:0000649
0	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SOFA	small_subunit_rRNA	SOFA	\N	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	42828	SO:0000650	\N	small_subunit_rRNA	SO:0000650
0	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SOFA	large_subunit_rRNA	SOFA	\N	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	42829	SO:0000651	\N	large_subunit_rRNA	SO:0000651
0	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SOFA	rRNA_5S	SOFA	\N	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	42830	SO:0000652	\N	rRNA_5S	SO:0000652
0	"A component of the large ribosomal subunit." [SO:ke]	SOFA	rRNA_28S	SOFA	\N	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	42831	SO:0000653	\N	rRNA_28S	SO:0000653
0	"A mitochondrial gene located in a maxicircle." [SO:xp]	\N	maxicircle_gene	\N	\N	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	42832	SO:0000654	\N	maxicircle_gene	SO:0000654
0	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	\N	sequence	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SO	42833	SO:0000655	\N	ncRNA	SO:0000655
0	"" []	\N	stRNA_encoding	\N	\N	sequence	"" []	SO	42834	SO:0000656	\N	stRNA_encoding	SO:0000656
0	"A region of sequence containing one or more repeat units." [SO:ke]	SOFA	repeat_region	SOFA	\N	sequence	"A region of sequence containing one or more repeat units." [SO:ke]	SO	42835	SO:0000657	\N	repeat_region	SO:0000657
0	"A repeat that is located at dispersed sites in the genome." [SO:ke]	SOFA	dispersed_repeat	SOFA	\N	sequence	"A repeat that is located at dispersed sites in the genome." [SO:ke]	SO	42836	SO:0000658	\N	dispersed_repeat	SO:0000658
0	"" []	\N	tmRNA_encoding	\N	\N	sequence	"" []	SO	42837	SO:0000659	\N	tmRNA_encoding	SO:0000659
0	"An intron which is spliced by the spliceosome." [SO:ke]	SOFA	spliceosomal_intron	SOFA	\N	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	42838	SO:0000662	\N	spliceosomal_intron	SO:0000662
0	"" []	\N	tRNA_encoding	\N	\N	sequence	"" []	SO	42839	SO:0000663	\N	tRNA_encoding	SO:0000663
0	"" []	\N	introgressed_chromosome_region	\N	\N	sequence	"" []	SO	42840	SO:0000664	\N	introgressed_chromosome_region	SO:0000664
0	"A transcript that is monocistronic." [SO:xp]	\N	monocistronic_transcript	\N	\N	sequence	"A transcript that is monocistronic." [SO:xp]	SO	42841	SO:0000665	\N	monocistronic_transcript	SO:0000665
0	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	\N	mobile_intron	\N	\N	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	42842	SO:0000666	\N	mobile_intron	SO:0000666
0	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	DBVAR,SOFA	insertion	DBVAR,SOFA	\N	sequence	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	SO	42843	SO:0000667	\N	insertion	SO:0000667
0	"A match against an EST sequence." [SO:ke]	SOFA	EST_match	SOFA	\N	sequence	"A match against an EST sequence." [SO:ke]	SO	42844	SO:0000668	\N	EST_match	SO:0000668
0	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	42845	SO:0000669	\N	sequence_rearrangement_feature	SO:0000669
0	"A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]	\N	chromosome_breakage_sequence	\N	\N	sequence	"A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]	SO	42846	SO:0000670	\N	chromosome_breakage_sequence	SO:0000670
0	"A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]	\N	internal_eliminated_sequence	\N	\N	sequence	"A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]	SO	42847	SO:0000671	\N	internal_eliminated_sequence	SO:0000671
0	"A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]	\N	macronucleus_destined_segment	\N	\N	sequence	"A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]	SO	42848	SO:0000672	\N	macronucleus_destined_segment	SO:0000672
0	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	\N	sequence	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SO	42849	SO:0000673	\N	transcript	SO:0000673
0	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	\N	canonical_three_prime_splice_site	\N	\N	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	42850	SO:0000676	\N	canonical_three_prime_splice_site	SO:0000676
0	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	\N	canonical_five_prime_splice_site	\N	\N	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	42851	SO:0000677	\N	canonical_five_prime_splice_site	SO:0000677
0	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	\N	non_canonical_three_prime_splice_site	\N	\N	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	42852	SO:0000678	\N	non_canonical_three_prime_splice_site	SO:0000678
0	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	\N	non_canonical_five_prime_splice_site	\N	\N	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	42853	SO:0000679	\N	non_canonical_five_prime_splice_site	SO:0000679
0	"A start codon that is not the usual AUG sequence." [SO:ke]	\N	non_canonical_start_codon	\N	\N	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	42854	SO:0000680	\N	non_canonical_start_codon	SO:0000680
0	"A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons." [SO:ke]	\N	aberrant_processed_transcript	\N	\N	sequence	"A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons." [SO:ke]	SO	42855	SO:0000681	\N	aberrant_processed_transcript	SO:0000681
0	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	\N	exonic_splice_enhancer	\N	\N	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	42856	SO:0000683	\N	exonic_splice_enhancer	SO:0000683
0	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SOFA	nuclease_sensitive_site	SOFA	\N	sequence	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SO	42857	SO:0000684	\N	nuclease_sensitive_site	SO:0000684
0	"" []	\N	DNAseI_hypersensitive_site	\N	\N	sequence	"" []	SO	42858	SO:0000685	\N	DNAseI_hypersensitive_site	SO:0000685
0	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	\N	translocation_element	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	42859	SO:0000686	\N	translocation_element	SO:0000686
0	"The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]	SOFA	deletion_junction	SOFA	\N	sequence	"The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]	SO	42860	SO:0000687	\N	deletion_junction	SO:0000687
0	"A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]	SOFA	golden_path	SOFA	\N	sequence	"A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]	SO	42861	SO:0000688	\N	golden_path	SO:0000688
0	"A match against cDNA sequence." [SO:ke]	SOFA	cDNA_match	SOFA	\N	sequence	"A match against cDNA sequence." [SO:ke]	SO	42862	SO:0000689	\N	cDNA_match	SO:0000689
0	"A gene that encodes a polycistronic transcript." [SO:xp]	\N	gene_with_polycistronic_transcript	\N	\N	sequence	"A gene that encodes a polycistronic transcript." [SO:xp]	SO	42863	SO:0000690	\N	gene_with_polycistronic_transcript	SO:0000690
0	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	biosapiens	cleaved_initiator_methionine	biosapiens	\N	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	42864	SO:0000691	\N	cleaved_initiator_methionine	SO:0000691
0	"A gene that encodes a dicistronic transcript." [SO:xp]	\N	gene_with_dicistronic_transcript	\N	\N	sequence	"A gene that encodes a dicistronic transcript." [SO:xp]	SO	42865	SO:0000692	\N	gene_with_dicistronic_transcript	SO:0000692
0	"A gene that encodes an mRNA that is recoded." [SO:xp]	\N	gene_with_recoded_mRNA	\N	\N	sequence	"A gene that encodes an mRNA that is recoded." [SO:xp]	SO	42866	SO:0000693	\N	gene_with_recoded_mRNA	SO:0000693
0	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SOFA	SNP	SOFA	\N	sequence	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SO	42867	SO:0000694	\N	SNP	SO:0000694
0	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	\N	sequence	"A sequence used in experiment." [SO:ke]	SO	42868	SO:0000695	\N	reagent	SO:0000695
0	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	\N	sequence	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SO	42869	SO:0000696	\N	oligo	SO:0000696
0	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	\N	gene_with_stop_codon_read_through	\N	\N	sequence	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	SO	42870	SO:0000697	\N	gene_with_stop_codon_read_through	SO:0000697
0	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	\N	gene_with_stop_codon_redefined_as_pyrrolysine	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	42871	SO:0000698	\N	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0000698
0	"A sequence_feature with an extent of zero." [SO:ke]	SOFA	junction	SOFA	\N	sequence	"A sequence_feature with an extent of zero." [SO:ke]	SO	42872	SO:0000699	\N	junction	SO:0000699
0	"A comment about the sequence." [SO:ke]	SOFA	remark	SOFA	\N	sequence	"A comment about the sequence." [SO:ke]	SO	42873	SO:0000700	\N	remark	SO:0000700
0	"A region of sequence where the validity of the base calling is questionable." [SO:ke]	SOFA	possible_base_call_error	SOFA	\N	sequence	"A region of sequence where the validity of the base calling is questionable." [SO:ke]	SO	42874	SO:0000701	\N	possible_base_call_error	SO:0000701
0	"A region of sequence where there may have been an error in the assembly." [SO:ke]	SOFA	possible_assembly_error	SOFA	\N	sequence	"A region of sequence where there may have been an error in the assembly." [SO:ke]	SO	42875	SO:0000702	\N	possible_assembly_error	SO:0000702
0	"A region of sequence implicated in an experimental result." [SO:ke]	SOFA	experimental_result_region	SOFA	\N	sequence	"A region of sequence implicated in an experimental result." [SO:ke]	SO	42876	SO:0000703	\N	experimental_result_region	SO:0000703
0	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	SOFA	gene	SOFA	\N	sequence	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	SO	42877	SO:0000704	\N	gene	SO:0000704
0	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SOFA	tandem_repeat	SOFA	\N	sequence	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SO	42878	SO:0000705	\N	tandem_repeat	SO:0000705
0	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SOFA	trans_splice_acceptor_site	SOFA	\N	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	42879	SO:0000706	\N	trans_splice_acceptor_site	SO:0000706
0	"The 5' five prime splice site region of the donor RNA." [SO:ke]	\N	trans_splice_donor_site	\N	\N	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	42880	SO:0000707	\N	trans_splice_donor_site	SO:0000707
0	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	\N	SL1_acceptor_site	\N	\N	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	42881	SO:0000708	\N	SL1_acceptor_site	SO:0000708
0	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	42882	SO:0000709	\N	SL2_acceptor_site	SO:0000709
0	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	\N	gene_with_stop_codon_redefined_as_selenocysteine	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	SO	42883	SO:0000710	\N	gene_with_stop_codon_redefined_as_selenocysteine	SO:0000710
0	"A gene with mRNA recoded by translational bypass." [SO:xp]	\N	gene_with_mRNA_recoded_by_translational_bypass	\N	\N	sequence	"A gene with mRNA recoded by translational bypass." [SO:xp]	SO	42884	SO:0000711	\N	gene_with_mRNA_recoded_by_translational_bypass	SO:0000711
0	"A gene encoding a transcript that has a translational frameshift." [SO:xp]	\N	gene_with_transcript_with_translational_frameshift	\N	\N	sequence	"A gene encoding a transcript that has a translational frameshift." [SO:xp]	SO	42885	SO:0000712	\N	gene_with_transcript_with_translational_frameshift	SO:0000712
0	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A motif that is active in the DNA form of the sequence." [SO:ke]	SO	42886	SO:0000713	\N	DNA_motif	SO:0000713
0	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	SOFA	nucleotide_motif	SOFA	\N	sequence	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	SO	42887	SO:0000714	\N	nucleotide_motif	SO:0000714
0	"A motif that is active in RNA sequence." [SO:ke]	SOFA	RNA_motif	SOFA	\N	sequence	"A motif that is active in RNA sequence." [SO:ke]	SO	42888	SO:0000715	\N	RNA_motif	SO:0000715
0	"An mRNA that has the quality dicistronic." [SO:ke]	\N	dicistronic_mRNA	\N	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	42889	SO:0000716	\N	dicistronic_mRNA	SO:0000716
0	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	SOFA	reading_frame	SOFA	\N	sequence	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	SO	42890	SO:0000717	\N	reading_frame	SO:0000717
0	"A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]	\N	blocked_reading_frame	\N	\N	sequence	"A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]	SO	42891	SO:0000718	\N	blocked_reading_frame	SO:0000718
0	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SOFA	ultracontig	SOFA	\N	sequence	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SO	42892	SO:0000719	\N	ultracontig	SO:0000719
0	"A transposable element that is foreign." [SO:ke]	\N	foreign_transposable_element	\N	\N	sequence	"A transposable element that is foreign." [SO:ke]	SO	42893	SO:0000720	\N	foreign_transposable_element	SO:0000720
0	"A gene that encodes a dicistronic primary transcript." [SO:xp]	\N	gene_with_dicistronic_primary_transcript	\N	\N	sequence	"A gene that encodes a dicistronic primary transcript." [SO:xp]	SO	42894	SO:0000721	\N	gene_with_dicistronic_primary_transcript	SO:0000721
0	"A gene that encodes a polycistronic mRNA." [SO:xp]	\N	gene_with_dicistronic_mRNA	\N	\N	sequence	"A gene that encodes a polycistronic mRNA." [SO:xp]	SO	42895	SO:0000722	\N	gene_with_dicistronic_mRNA	SO:0000722
0	"Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]	\N	iDNA	\N	\N	sequence	"Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]	SO	42896	SO:0000723	\N	iDNA	SO:0000723
0	"A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	oriT	SOFA	\N	sequence	"A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42897	SO:0000724	\N	oriT	SO:0000724
0	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	biosapiens,SOFA	transit_peptide	biosapiens,SOFA	\N	sequence	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	42898	SO:0000725	\N	transit_peptide	SO:0000725
0	"The simplest repeated component of a repeat region. A single repeat." [SO:ke]	\N	repeat_unit	\N	\N	sequence	"The simplest repeated component of a repeat region. A single repeat." [SO:ke]	SO	42899	SO:0000726	\N	repeat_unit	SO:0000726
0	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SOFA	CRM	SOFA	\N	sequence	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SO	42900	SO:0000727	\N	CRM	SO:0000727
0	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	\N	intein	\N	\N	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	42901	SO:0000728	\N	intein	SO:0000728
0	"An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]	\N	intein_containing	\N	\N	sequence	"An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]	SO	42902	SO:0000729	\N	intein_containing	SO:0000729
0	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SOFA	gap	SOFA	\N	sequence	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SO	42903	SO:0000730	\N	gap	SO:0000730
0	"An attribute to describe a feature that is incomplete." [SO:ke]	\N	fragmentary	\N	\N	sequence	"An attribute to describe a feature that is incomplete." [SO:ke]	SO	42904	SO:0000731	\N	fragmentary	SO:0000731
0	"An attribute describing an unverified region." [SO:ke]	\N	predicted	\N	\N	sequence	"An attribute describing an unverified region." [SO:ke]	SO	42905	SO:0000732	\N	predicted	SO:0000732
0	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a located_sequence_feature." [SO:ke]	SO	42906	SO:0000733	\N	feature_attribute	SO:0000733
0	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	\N	exemplar_mRNA	\N	\N	sequence	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	42907	SO:0000734	\N	exemplar_mRNA	SO:0000734
0	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	42908	SO:0000735	\N	sequence_location	SO:0000735
0	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	42909	SO:0000736	\N	organelle_sequence	SO:0000736
0	"" []	\N	mitochondrial_sequence	\N	\N	sequence	"" []	SO	42910	SO:0000737	\N	mitochondrial_sequence	SO:0000737
0	"" []	\N	nuclear_sequence	\N	\N	sequence	"" []	SO	42911	SO:0000738	\N	nuclear_sequence	SO:0000738
0	"" []	\N	nucleomorphic_sequence	\N	\N	sequence	"" []	SO	42912	SO:0000739	\N	nucleomorphic_sequence	SO:0000739
0	"" []	\N	plastid_sequence	\N	\N	sequence	"" []	SO	42913	SO:0000740	\N	plastid_sequence	SO:0000740
0	"A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055]	\N	kinetoplast	\N	\N	sequence	"A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055]	SO	42914	SO:0000741	\N	kinetoplast	SO:0000741
0	"A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]	\N	maxicircle	\N	\N	sequence	"A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]	SO	42915	SO:0000742	\N	maxicircle	SO:0000742
0	"" []	\N	apicoplast_sequence	\N	\N	sequence	"" []	SO	42916	SO:0000743	\N	apicoplast_sequence	SO:0000743
0	"" []	\N	chromoplast_sequence	\N	\N	sequence	"" []	SO	42917	SO:0000744	\N	chromoplast_sequence	SO:0000744
0	"" []	\N	chloroplast_sequence	\N	\N	sequence	"" []	SO	42918	SO:0000745	\N	chloroplast_sequence	SO:0000745
0	"" []	\N	cyanelle_sequence	\N	\N	sequence	"" []	SO	42919	SO:0000746	\N	cyanelle_sequence	SO:0000746
0	"" []	\N	leucoplast_sequence	\N	\N	sequence	"" []	SO	42920	SO:0000747	\N	leucoplast_sequence	SO:0000747
0	"" []	\N	proplastid_sequence	\N	\N	sequence	"" []	SO	42921	SO:0000748	\N	proplastid_sequence	SO:0000748
0	"" []	\N	plasmid_location	\N	\N	sequence	"" []	SO	42922	SO:0000749	\N	plasmid_location	SO:0000749
0	"An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]	\N	amplification_origin	\N	\N	sequence	"An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]	SO	42923	SO:0000750	\N	amplification_origin	SO:0000750
0	"" []	\N	proviral_location	\N	\N	sequence	"" []	SO	42924	SO:0000751	\N	proviral_location	SO:0000751
0	"" []	SOFA	gene_group_regulatory_region	SOFA	\N	sequence	"" []	SO	42925	SO:0000752	\N	gene_group_regulatory_region	SO:0000752
0	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SOFA	clone_insert	SOFA	\N	sequence	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SO	42926	SO:0000753	\N	clone_insert	SO:0000753
0	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	\N	lambda_vector	\N	\N	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	42927	SO:0000754	\N	lambda_vector	SO:0000754
0	"" []	\N	plasmid_vector	\N	\N	sequence	"" []	SO	42928	SO:0000755	\N	plasmid_vector	SO:0000755
0	"DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]	\N	cDNA	\N	\N	sequence	"DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]	SO	42929	SO:0000756	\N	cDNA	SO:0000756
0	"" []	\N	single_stranded_cDNA	\N	\N	sequence	"" []	SO	42930	SO:0000757	\N	single_stranded_cDNA	SO:0000757
0	"" []	\N	double_stranded_cDNA	\N	\N	sequence	"" []	SO	42931	SO:0000758	\N	double_stranded_cDNA	SO:0000758
0	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	\N	pyrrolysyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	42932	SO:0000766	\N	pyrrolysyl_tRNA	SO:0000766
0	"A plasmid that may integrate with a chromosome." [SO:ma]	\N	episome	\N	\N	sequence	"A plasmid that may integrate with a chromosome." [SO:ma]	SO	42933	SO:0000768	\N	episome	SO:0000768
0	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	\N	tmRNA_coding_piece	\N	\N	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	42934	SO:0000769	\N	tmRNA_coding_piece	SO:0000769
0	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	\N	tmRNA_acceptor_piece	\N	\N	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	42935	SO:0000770	\N	tmRNA_acceptor_piece	SO:0000770
0	"A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]	\N	QTL	\N	\N	sequence	"A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]	SO	42936	SO:0000771	\N	QTL	SO:0000771
0	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	\N	genomic_island	\N	\N	sequence	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	SO	42937	SO:0000772	\N	genomic_island	SO:0000772
0	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	\N	pathogenic_island	\N	\N	sequence	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	SO	42938	SO:0000773	\N	pathogenic_island	SO:0000773
0	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	\N	metabolic_island	\N	\N	sequence	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	42939	SO:0000774	\N	metabolic_island	SO:0000774
0	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	\N	adaptive_island	\N	\N	sequence	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	SO	42940	SO:0000775	\N	adaptive_island	SO:0000775
0	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	\N	symbiosis_island	\N	\N	sequence	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	42941	SO:0000776	\N	symbiosis_island	SO:0000776
0	"A non functional descendant of an rRNA." [SO:ke]	SOFA	pseudogenic_rRNA	SOFA	\N	sequence	"A non functional descendant of an rRNA." [SO:ke]	SO	42942	SO:0000777	\N	pseudogenic_rRNA	SO:0000777
0	"A non functional descendent of a tRNA." [SO:ke]	SOFA	pseudogenic_tRNA	SOFA	\N	sequence	"A non functional descendent of a tRNA." [SO:ke]	SO	42943	SO:0000778	\N	pseudogenic_tRNA	SO:0000778
0	"An episome that is engineered." [SO:xp]	\N	engineered_episome	\N	\N	sequence	"An episome that is engineered." [SO:xp]	SO	42944	SO:0000779	\N	engineered_episome	SO:0000779
0	"Attribute describing sequence that has been integrated with foreign sequence." [SO:ke]	\N	transgenic	\N	\N	sequence	"Attribute describing sequence that has been integrated with foreign sequence." [SO:ke]	SO	42945	SO:0000781	\N	transgenic	SO:0000781
0	"An attribute describing a feature that occurs in nature." [SO:ke]	\N	natural	\N	\N	sequence	"An attribute describing a feature that occurs in nature." [SO:ke]	SO	42946	SO:0000782	\N	natural	SO:0000782
0	"An attribute to describe a region that was modified in vitro." [SO:ke]	\N	engineered	\N	\N	sequence	"An attribute to describe a region that was modified in vitro." [SO:ke]	SO	42947	SO:0000783	\N	engineered	SO:0000783
0	"An attribute to describe a region from another species." [SO:ke]	\N	foreign	\N	\N	sequence	"An attribute to describe a region from another species." [SO:ke]	SO	42948	SO:0000784	\N	foreign	SO:0000784
0	"" []	\N	cloned_region	\N	\N	sequence	"" []	SO	42949	SO:0000785	\N	cloned_region	SO:0000785
0	"An attribute to describe a feature that has been proven." [SO:ke]	\N	validated	\N	\N	sequence	"An attribute to describe a feature that has been proven." [SO:ke]	SO	42950	SO:0000789	\N	validated	SO:0000789
0	"An attribute describing a feature that is invalidated." [SO:ke]	\N	invalidated	\N	\N	sequence	"An attribute describing a feature that is invalidated." [SO:ke]	SO	42951	SO:0000790	\N	invalidated	SO:0000790
0	"A rescue region that is engineered." [SO:xp]	\N	engineered_rescue_region	\N	\N	sequence	"A rescue region that is engineered." [SO:xp]	SO	42952	SO:0000794	\N	engineered_rescue_region	SO:0000794
0	"A mini_gene that rescues." [SO:xp]	\N	rescue_mini_gene	\N	\N	sequence	"A mini_gene that rescues." [SO:xp]	SO	42953	SO:0000795	\N	rescue_mini_gene	SO:0000795
0	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	\N	transgenic_transposable_element	\N	\N	sequence	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	SO	42954	SO:0000796	\N	transgenic_transposable_element	SO:0000796
0	"TE that exists (or existed) in nature." [FB:mc]	\N	natural_transposable_element	\N	\N	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	42955	SO:0000797	\N	natural_transposable_element	SO:0000797
0	"TE that has been modified by manipulations in vitro." [FB:mc]	\N	engineered_transposable_element	\N	\N	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	42956	SO:0000798	\N	engineered_transposable_element	SO:0000798
0	"A transposable_element that is engineered and foreign." [FB:mc]	\N	engineered_foreign_transposable_element	\N	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	42957	SO:0000799	\N	engineered_foreign_transposable_element	SO:0000799
0	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	\N	assortment_derived_duplication	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	42958	SO:0000800	\N	assortment_derived_duplication	SO:0000800
0	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	\N	assortment_derived_deficiency_plus_duplication	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	42959	SO:0000801	\N	assortment_derived_deficiency_plus_duplication	SO:0000801
0	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	\N	assortment_derived_deficiency	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	42960	SO:0000802	\N	assortment_derived_deficiency	SO:0000802
0	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	\N	assortment_derived_aneuploid	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	42961	SO:0000803	\N	assortment_derived_aneuploid	SO:0000803
0	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A region that is engineered." [SO:xp]	SO	42962	SO:0000804	\N	engineered_region	SO:0000804
0	"A region that is engineered and foreign." [SO:xp]	\N	engineered_foreign_region	\N	\N	sequence	"A region that is engineered and foreign." [SO:xp]	SO	42963	SO:0000805	\N	engineered_foreign_region	SO:0000805
0	"" []	\N	fusion	\N	\N	sequence	"" []	SO	42964	SO:0000806	\N	fusion	SO:0000806
0	"A tag that is engineered." [SO:xp]	\N	engineered_tag	\N	\N	sequence	"A tag that is engineered." [SO:xp]	SO	42965	SO:0000807	\N	engineered_tag	SO:0000807
0	"A cDNA clone that has been validated." [SO:xp]	\N	validated_cDNA_clone	\N	\N	sequence	"A cDNA clone that has been validated." [SO:xp]	SO	42966	SO:0000808	\N	validated_cDNA_clone	SO:0000808
0	"A cDNA clone that is invalid." [SO:xp]	\N	invalidated_cDNA_clone	\N	\N	sequence	"A cDNA clone that is invalid." [SO:xp]	SO	42967	SO:0000809	\N	invalidated_cDNA_clone	SO:0000809
0	"A cDNA clone invalidated because it is chimeric." [SO:xp]	\N	chimeric_cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated because it is chimeric." [SO:xp]	SO	42968	SO:0000810	\N	chimeric_cDNA_clone	SO:0000810
0	"A cDNA clone invalidated by genomic contamination." [SO:xp]	\N	genomically_contaminated_cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated by genomic contamination." [SO:xp]	SO	42969	SO:0000811	\N	genomically_contaminated_cDNA_clone	SO:0000811
0	"A cDNA clone invalidated by polyA priming." [SO:xp]	\N	polyA_primed_cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated by polyA priming." [SO:xp]	SO	42970	SO:0000812	\N	polyA_primed_cDNA_clone	SO:0000812
0	"A cDNA invalidated clone by partial processing." [SO:xp]	\N	partially_processed_cDNA_clone	\N	\N	sequence	"A cDNA invalidated clone by partial processing." [SO:xp]	SO	42971	SO:0000813	\N	partially_processed_cDNA_clone	SO:0000813
0	"An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]	\N	rescue	\N	\N	sequence	"An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]	SO	42972	SO:0000814	\N	rescue	SO:0000814
0	"By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]	\N	mini_gene	\N	\N	sequence	"By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]	SO	42973	SO:0000815	\N	mini_gene	SO:0000815
0	"A gene that rescues." [SO:xp]	\N	rescue_gene	\N	\N	sequence	"A gene that rescues." [SO:xp]	SO	42974	SO:0000816	\N	rescue_gene	SO:0000816
0	"An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]	\N	wild_type	\N	\N	sequence	"An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]	SO	42975	SO:0000817	\N	wild_type	SO:0000817
0	"A gene that rescues." [SO:xp]	\N	wild_type_rescue_gene	\N	\N	sequence	"A gene that rescues." [SO:xp]	SO	42976	SO:0000818	\N	wild_type_rescue_gene	SO:0000818
0	"A chromosome originating in a mitochondria." [SO:xp]	\N	mitochondrial_chromosome	\N	\N	sequence	"A chromosome originating in a mitochondria." [SO:xp]	SO	42977	SO:0000819	\N	mitochondrial_chromosome	SO:0000819
0	"A chromosome originating in a chloroplast." [SO:xp]	\N	chloroplast_chromosome	\N	\N	sequence	"A chromosome originating in a chloroplast." [SO:xp]	SO	42978	SO:0000820	\N	chloroplast_chromosome	SO:0000820
0	"A chromosome originating in a chromoplast." [SO:xp]	\N	chromoplast_chromosome	\N	\N	sequence	"A chromosome originating in a chromoplast." [SO:xp]	SO	42979	SO:0000821	\N	chromoplast_chromosome	SO:0000821
0	"A chromosome originating in a cyanelle." [SO:xp]	\N	cyanelle_chromosome	\N	\N	sequence	"A chromosome originating in a cyanelle." [SO:xp]	SO	42980	SO:0000822	\N	cyanelle_chromosome	SO:0000822
0	"A chromosome with origin in a leucoplast." [SO:xp]	\N	leucoplast_chromosome	\N	\N	sequence	"A chromosome with origin in a leucoplast." [SO:xp]	SO	42981	SO:0000823	\N	leucoplast_chromosome	SO:0000823
0	"A chromosome originating in a macronucleus." [SO:xp]	\N	macronuclear_chromosome	\N	\N	sequence	"A chromosome originating in a macronucleus." [SO:xp]	SO	42982	SO:0000824	\N	macronuclear_chromosome	SO:0000824
0	"A chromosome originating in a micronucleus." [SO:xp]	\N	micronuclear_chromosome	\N	\N	sequence	"A chromosome originating in a micronucleus." [SO:xp]	SO	42983	SO:0000825	\N	micronuclear_chromosome	SO:0000825
0	"A chromosome originating in a nucleus." [SO:xp]	\N	nuclear_chromosome	\N	\N	sequence	"A chromosome originating in a nucleus." [SO:xp]	SO	42984	SO:0000828	\N	nuclear_chromosome	SO:0000828
0	"A chromosome originating in a nucleomorph." [SO:xp]	\N	nucleomorphic_chromosome	\N	\N	sequence	"A chromosome originating in a nucleomorph." [SO:xp]	SO	42985	SO:0000829	\N	nucleomorphic_chromosome	SO:0000829
0	"A region of a chromosome." [SO:ke]	SOFA	chromosome_part	SOFA	\N	sequence	"A region of a chromosome." [SO:ke]	SO	42986	SO:0000830	\N	chromosome_part	SO:0000830
0	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	\N	sequence	"A region of a gene." [SO:ke]	SO	42987	SO:0000831	\N	gene_member_region	SO:0000831
0	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	\N	sequence	"A region of a transcript." [SO:ke]	SO	42988	SO:0000833	\N	transcript_region	SO:0000833
0	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	\N	sequence	"A region of a mature transcript." [SO:ke]	SO	42989	SO:0000834	\N	mature_transcript_region	SO:0000834
0	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	\N	sequence	"A part of a primary transcript." [SO:ke]	SO	42990	SO:0000835	\N	primary_transcript_region	SO:0000835
0	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	\N	sequence	"A region of an mRNA." [SO:cb]	SO	42991	SO:0000836	\N	mRNA_region	SO:0000836
0	"A region of UTR." [SO:ke]	SOFA	UTR_region	SOFA	\N	sequence	"A region of UTR." [SO:ke]	SO	42992	SO:0000837	\N	UTR_region	SO:0000837
0	"A region of an rRNA primary transcript." [SO:ke]	\N	rRNA_primary_transcript_region	\N	\N	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	42993	SO:0000838	\N	rRNA_primary_transcript_region	SO:0000838
0	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	\N	sequence	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	SO	42994	SO:0000839	\N	polypeptide_region	SO:0000839
0	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"A region of a repeated sequence." [SO:ke]	SO	42995	SO:0000840	\N	repeat_component	SO:0000840
0	"A region within an intron." [SO:ke]	SOFA	spliceosomal_intron_region	SOFA	\N	sequence	"A region within an intron." [SO:ke]	SO	42996	SO:0000841	\N	spliceosomal_intron_region	SO:0000841
0	"" []	SOFA	gene_component_region	SOFA	\N	sequence	"" []	SO	42997	SO:0000842	\N	gene_component_region	SO:0000842
0	"A region of a tmRNA." [SO:cb]	\N	tmRNA_region	\N	\N	sequence	"A region of a tmRNA." [SO:cb]	SO	42998	SO:0000847	\N	tmRNA_region	SO:0000847
0	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	42999	SO:0000848	\N	LTR_component	SO:0000848
0	"" []	\N	three_prime_LTR_component	\N	\N	sequence	"" []	SO	43000	SO:0000849	\N	three_prime_LTR_component	SO:0000849
0	"" []	\N	five_prime_LTR_component	\N	\N	sequence	"" []	SO	43001	SO:0000850	\N	five_prime_LTR_component	SO:0000850
0	"A region of a CDS." [SO:cb]	SOFA	CDS_region	SOFA	\N	sequence	"A region of a CDS." [SO:cb]	SO	43002	SO:0000851	\N	CDS_region	SO:0000851
0	"A region of an exon." [RSC:cb]	SOFA	exon_region	SOFA	\N	sequence	"A region of an exon." [RSC:cb]	SO	43003	SO:0000852	\N	exon_region	SO:0000852
0	"A region that is homologous to another region." [SO:ke]	\N	homologous_region	\N	\N	sequence	"A region that is homologous to another region." [SO:ke]	SO	43004	SO:0000853	\N	homologous_region	SO:0000853
0	"A homologous_region that is paralogous to another region." [SO:ke]	\N	paralogous_region	\N	\N	sequence	"A homologous_region that is paralogous to another region." [SO:ke]	SO	43005	SO:0000854	\N	paralogous_region	SO:0000854
0	"A homologous_region that is orthologous to another region." [SO:ke]	\N	orthologous_region	\N	\N	sequence	"A homologous_region that is orthologous to another region." [SO:ke]	SO	43006	SO:0000855	\N	orthologous_region	SO:0000855
0	"" []	\N	conserved	\N	\N	sequence	"" []	SO	43007	SO:0000856	\N	conserved	SO:0000856
0	"Similarity due to common ancestry." [SO:ke]	\N	homologous	\N	\N	sequence	"Similarity due to common ancestry." [SO:ke]	SO	43008	SO:0000857	\N	homologous	SO:0000857
0	"An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]	\N	orthologous	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]	SO	43009	SO:0000858	\N	orthologous	SO:0000858
0	"An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]	\N	paralogous	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]	SO	43010	SO:0000859	\N	paralogous	SO:0000859
0	"Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]	\N	syntenic	\N	\N	sequence	"Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]	SO	43011	SO:0000860	\N	syntenic	SO:0000860
0	"A primary transcript that is capped." [SO:xp]	\N	capped_primary_transcript	\N	\N	sequence	"A primary transcript that is capped." [SO:xp]	SO	43012	SO:0000861	\N	capped_primary_transcript	SO:0000861
0	"An mRNA that is capped." [SO:xp]	\N	capped_mRNA	\N	\N	sequence	"An mRNA that is capped." [SO:xp]	SO	43013	SO:0000862	\N	capped_mRNA	SO:0000862
0	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"An attribute describing an mRNA feature." [SO:ke]	SO	43014	SO:0000863	\N	mRNA_attribute	SO:0000863
0	"An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]	\N	exemplar	\N	\N	sequence	"An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]	SO	43015	SO:0000864	\N	exemplar	SO:0000864
0	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	\N	frameshift	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	SO	43016	SO:0000865	\N	frameshift	SO:0000865
0	"A frameshift caused by deleting one base." [SO:ke]	\N	minus_1_frameshift	\N	\N	sequence	"A frameshift caused by deleting one base." [SO:ke]	SO	43017	SO:0000866	\N	minus_1_frameshift	SO:0000866
0	"A frameshift caused by deleting two bases." [SO:ke]	\N	minus_2_frameshift	\N	\N	sequence	"A frameshift caused by deleting two bases." [SO:ke]	SO	43018	SO:0000867	\N	minus_2_frameshift	SO:0000867
0	"A frameshift caused by inserting one base." [SO:ke]	\N	plus_1_frameshift	\N	\N	sequence	"A frameshift caused by inserting one base." [SO:ke]	SO	43019	SO:0000868	\N	plus_1_frameshift	SO:0000868
0	"A frameshift caused by inserting two bases." [SO:ke]	\N	plus_2_framshift	\N	\N	sequence	"A frameshift caused by inserting two bases." [SO:ke]	SO	43020	SO:0000869	\N	plus_2_framshift	SO:0000869
0	"An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]	\N	trans_spliced	\N	\N	sequence	"An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]	SO	43021	SO:0000870	\N	trans_spliced	SO:0000870
0	"An mRNA that is polyadenylated." [SO:xp]	\N	polyadenylated_mRNA	\N	\N	sequence	"An mRNA that is polyadenylated." [SO:xp]	SO	43022	SO:0000871	\N	polyadenylated_mRNA	SO:0000871
0	"An mRNA that is trans-spliced." [SO:xp]	\N	trans_spliced_mRNA	\N	\N	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	43023	SO:0000872	\N	trans_spliced_mRNA	SO:0000872
0	"A transcript that is edited." [SO:ke]	\N	edited_transcript	\N	\N	sequence	"A transcript that is edited." [SO:ke]	SO	43024	SO:0000873	\N	edited_transcript	SO:0000873
0	"A transcript that has been edited by A to I substitution." [SO:ke]	\N	edited_transcript_by_A_to_I_substitution	\N	\N	sequence	"A transcript that has been edited by A to I substitution." [SO:ke]	SO	43025	SO:0000874	\N	edited_transcript_by_A_to_I_substitution	SO:0000874
0	"An attribute describing a sequence that is bound by a protein." [SO:ke]	\N	bound_by_protein	\N	\N	sequence	"An attribute describing a sequence that is bound by a protein." [SO:ke]	SO	43026	SO:0000875	\N	bound_by_protein	SO:0000875
0	"An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]	\N	bound_by_nucleic_acid	\N	\N	sequence	"An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]	SO	43027	SO:0000876	\N	bound_by_nucleic_acid	SO:0000876
0	"An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]	\N	alternatively_spliced	\N	\N	sequence	"An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]	SO	43028	SO:0000877	\N	alternatively_spliced	SO:0000877
0	"An attribute describing a sequence that contains the code for one gene product." [SO:ke]	\N	monocistronic	\N	\N	sequence	"An attribute describing a sequence that contains the code for one gene product." [SO:ke]	SO	43029	SO:0000878	\N	monocistronic	SO:0000878
0	"An attribute describing a sequence that contains the code for two gene products." [SO:ke]	\N	dicistronic	\N	\N	sequence	"An attribute describing a sequence that contains the code for two gene products." [SO:ke]	SO	43030	SO:0000879	\N	dicistronic	SO:0000879
0	"An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]	\N	polycistronic	\N	\N	sequence	"An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]	SO	43031	SO:0000880	\N	polycistronic	SO:0000880
0	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	\N	recoded	\N	\N	sequence	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	SO	43032	SO:0000881	\N	recoded	SO:0000881
0	"An attribute describing the alteration of codon meaning." [SO:ke]	\N	codon_redefined	\N	\N	sequence	"An attribute describing the alteration of codon meaning." [SO:ke]	SO	43033	SO:0000882	\N	codon_redefined	SO:0000882
0	"A stop codon redefined to be a new amino acid." [SO:ke]	\N	stop_codon_read_through	\N	\N	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	43034	SO:0000883	\N	stop_codon_read_through	SO:0000883
0	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	\N	stop_codon_redefined_as_pyrrolysine	\N	\N	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	43035	SO:0000884	\N	stop_codon_redefined_as_pyrrolysine	SO:0000884
0	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	\N	stop_codon_redefined_as_selenocysteine	\N	\N	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	43036	SO:0000885	\N	stop_codon_redefined_as_selenocysteine	SO:0000885
0	"Recoded mRNA where a block of nucleotides is not translated." [SO:ke]	\N	recoded_by_translational_bypass	\N	\N	sequence	"Recoded mRNA where a block of nucleotides is not translated." [SO:ke]	SO	43037	SO:0000886	\N	recoded_by_translational_bypass	SO:0000886
0	"Recoding by frameshifting a particular site." [SO:ke]	\N	translationally_frameshifted	\N	\N	sequence	"Recoding by frameshifting a particular site." [SO:ke]	SO	43038	SO:0000887	\N	translationally_frameshifted	SO:0000887
0	"A gene that is maternally_imprinted." [SO:xp]	\N	maternally_imprinted_gene	\N	\N	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	43039	SO:0000888	\N	maternally_imprinted_gene	SO:0000888
0	"A gene that is paternally imprinted." [SO:xp]	\N	paternally_imprinted_gene	\N	\N	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	43040	SO:0000889	\N	paternally_imprinted_gene	SO:0000889
0	"A gene that is post translationally regulated." [SO:xp]	\N	post_translationally_regulated_gene	\N	\N	sequence	"A gene that is post translationally regulated." [SO:xp]	SO	43041	SO:0000890	\N	post_translationally_regulated_gene	SO:0000890
0	"A gene that is negatively autoreguated." [SO:xp]	\N	negatively_autoregulated_gene	\N	\N	sequence	"A gene that is negatively autoreguated." [SO:xp]	SO	43042	SO:0000891	\N	negatively_autoregulated_gene	SO:0000891
0	"A gene that is positively autoregulated." [SO:xp]	\N	positively_autoregulated_gene	\N	\N	sequence	"A gene that is positively autoregulated." [SO:xp]	SO	43043	SO:0000892	\N	positively_autoregulated_gene	SO:0000892
0	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	\N	silenced	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	SO	43044	SO:0000893	\N	silenced	SO:0000893
0	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	\N	silenced_by_DNA_modification	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	SO	43045	SO:0000894	\N	silenced_by_DNA_modification	SO:0000894
0	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	\N	silenced_by_DNA_methylation	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	43046	SO:0000895	\N	silenced_by_DNA_methylation	SO:0000895
0	"A gene that is translationally regulated." [SO:xp]	\N	translationally_regulated_gene	\N	\N	sequence	"A gene that is translationally regulated." [SO:xp]	SO	43047	SO:0000896	\N	translationally_regulated_gene	SO:0000896
0	"A gene that is allelically_excluded." [SO:xp]	\N	allelically_excluded_gene	\N	\N	sequence	"A gene that is allelically_excluded." [SO:xp]	SO	43048	SO:0000897	\N	allelically_excluded_gene	SO:0000897
0	"A gene that is epigenetically modified." [SO:ke]	\N	epigenetically_modified_gene	\N	\N	sequence	"A gene that is epigenetically modified." [SO:ke]	SO	43049	SO:0000898	\N	epigenetically_modified_gene	SO:0000898
0	"A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]	\N	transgene	\N	\N	sequence	"A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]	SO	43050	SO:0000902	\N	transgene	SO:0000902
0	"" []	\N	endogenous_retroviral_sequence	\N	\N	sequence	"" []	SO	43051	SO:0000903	\N	endogenous_retroviral_sequence	SO:0000903
0	"An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]	\N	rearranged_at_DNA_level	\N	\N	sequence	"An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]	SO	43052	SO:0000904	\N	rearranged_at_DNA_level	SO:0000904
0	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	SO	43053	SO:0000905	\N	status	SO:0000905
0	"Attribute to describe a feature that is independently known - not predicted." [SO:ke]	\N	independently_known	\N	\N	sequence	"Attribute to describe a feature that is independently known - not predicted." [SO:ke]	SO	43054	SO:0000906	\N	independently_known	SO:0000906
0	"An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]	\N	supported_by_sequence_similarity	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]	SO	43055	SO:0000907	\N	supported_by_sequence_similarity	SO:0000907
0	"An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]	\N	supported_by_domain_match	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]	SO	43056	SO:0000908	\N	supported_by_domain_match	SO:0000908
0	"An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]	\N	supported_by_EST_or_cDNA	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]	SO	43057	SO:0000909	\N	supported_by_EST_or_cDNA	SO:0000909
0	"" []	\N	orphan	\N	\N	sequence	"" []	SO	43058	SO:0000910	\N	orphan	SO:0000910
0	"An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]	\N	predicted_by_ab_initio_computation	\N	\N	sequence	"An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]	SO	43059	SO:0000911	\N	predicted_by_ab_initio_computation	SO:0000911
0	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn	biosapiens	\N	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43060	SO:0000912	\N	asx_turn	SO:0000912
0	"A clone insert made from cDNA." [SO:xp]	\N	cloned_cDNA_insert	\N	\N	sequence	"A clone insert made from cDNA." [SO:xp]	SO	43061	SO:0000913	\N	cloned_cDNA_insert	SO:0000913
0	"A clone insert made from genomic DNA." [SO:xp]	\N	cloned_genomic_insert	\N	\N	sequence	"A clone insert made from genomic DNA." [SO:xp]	SO	43062	SO:0000914	\N	cloned_genomic_insert	SO:0000914
0	"A clone insert that is engineered." [SO:xp]	\N	engineered_insert	\N	\N	sequence	"A clone insert that is engineered." [SO:xp]	SO	43063	SO:0000915	\N	engineered_insert	SO:0000915
0	"An mRNA that is edited." [SO:xp]	\N	edited_mRNA	\N	\N	sequence	"An mRNA that is edited." [SO:xp]	SO	43064	SO:0000929	\N	edited_mRNA	SO:0000929
0	"A region of guide RNA." [SO:ma]	\N	guide_RNA_region	\N	\N	sequence	"A region of guide RNA." [SO:ma]	SO	43065	SO:0000930	\N	guide_RNA_region	SO:0000930
0	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	\N	anchor_region	\N	\N	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	43066	SO:0000931	\N	anchor_region	SO:0000931
0	"" []	\N	pre_edited_mRNA	\N	\N	sequence	"" []	SO	43067	SO:0000932	\N	pre_edited_mRNA	SO:0000932
0	"An attribute to describe a feature between stages of processing." [SO:ke]	\N	intermediate	\N	\N	sequence	"An attribute to describe a feature between stages of processing." [SO:ke]	SO	43068	SO:0000933	\N	intermediate	SO:0000933
0	"A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]	\N	miRNA_target_site	\N	\N	sequence	"A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]	SO	43069	SO:0000934	\N	miRNA_target_site	SO:0000934
0	"A CDS that is edited." [SO:xp]	\N	edited_CDS	\N	\N	sequence	"A CDS that is edited." [SO:xp]	SO	43070	SO:0000935	\N	edited_CDS	SO:0000935
0	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	\N	\N	sequence	"" []	SO	43071	SO:0000936	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000936
0	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"" []	SO	43072	SO:0000938	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000938
0	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"" []	SO	43073	SO:0000939	\N	vertebrate_immune_system_gene_recombination_signal_feature	SO:0000939
0	"" []	\N	recombinationally_rearranged	\N	\N	sequence	"" []	SO	43074	SO:0000940	\N	recombinationally_rearranged	SO:0000940
0	"A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]	\N	recombinationally_rearranged_vertebrate_immune_system_gene	\N	\N	sequence	"A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]	SO	43075	SO:0000941	\N	recombinationally_rearranged_vertebrate_immune_system_gene	SO:0000941
0	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	\N	attP_site	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	43076	SO:0000942	\N	attP_site	SO:0000942
0	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	\N	attB_site	\N	\N	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	43077	SO:0000943	\N	attB_site	SO:0000943
0	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	\N	attL_site	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	43078	SO:0000944	\N	attL_site	SO:0000944
0	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	\N	attR_site	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	43079	SO:0000945	\N	attR_site	SO:0000945
0	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	\N	integration_excision_site	\N	\N	sequence	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	SO	43080	SO:0000946	\N	integration_excision_site	SO:0000946
0	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	\N	resolution_site	\N	\N	sequence	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	SO	43081	SO:0000947	\N	resolution_site	SO:0000947
0	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	\N	inversion_site	\N	\N	sequence	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	SO	43082	SO:0000948	\N	inversion_site	SO:0000948
0	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	\N	dif_site	\N	\N	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	43083	SO:0000949	\N	dif_site	SO:0000949
0	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	\N	attC_site	\N	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	43084	SO:0000950	\N	attC_site	SO:0000950
0	"" []	\N	eukaryotic_terminator	\N	\N	sequence	"" []	SO	43085	SO:0000951	\N	eukaryotic_terminator	SO:0000951
0	"An origin of vegetative replication in plasmids and phages." [SO:as]	\N	oriV	\N	\N	sequence	"An origin of vegetative replication in plasmids and phages." [SO:as]	SO	43086	SO:0000952	\N	oriV	SO:0000952
0	"An origin of bacterial chromosome replication." [SO:as]	\N	oriC	\N	\N	sequence	"An origin of bacterial chromosome replication." [SO:as]	SO	43087	SO:0000953	\N	oriC	SO:0000953
0	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	\N	DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	SO	43088	SO:0000954	\N	DNA_chromosome	SO:0000954
0	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	\N	double_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	SO	43089	SO:0000955	\N	double_stranded_DNA_chromosome	SO:0000955
0	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	\N	single_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	SO	43090	SO:0000956	\N	single_stranded_DNA_chromosome	SO:0000956
0	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	\N	linear_double_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	SO	43091	SO:0000957	\N	linear_double_stranded_DNA_chromosome	SO:0000957
0	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	\N	circular_double_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	SO	43092	SO:0000958	\N	circular_double_stranded_DNA_chromosome	SO:0000958
0	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	\N	linear_single_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	SO	43093	SO:0000959	\N	linear_single_stranded_DNA_chromosome	SO:0000959
0	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	\N	circular_single_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	43094	SO:0000960	\N	circular_single_stranded_DNA_chromosome	SO:0000960
0	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	\N	RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	SO	43095	SO:0000961	\N	RNA_chromosome	SO:0000961
0	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	\N	single_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	SO	43096	SO:0000962	\N	single_stranded_RNA_chromosome	SO:0000962
0	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	\N	linear_single_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	SO	43097	SO:0000963	\N	linear_single_stranded_RNA_chromosome	SO:0000963
0	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	\N	linear_double_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	SO	43098	SO:0000964	\N	linear_double_stranded_RNA_chromosome	SO:0000964
0	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	\N	double_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	SO	43099	SO:0000965	\N	double_stranded_RNA_chromosome	SO:0000965
0	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	\N	circular_single_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	43100	SO:0000966	\N	circular_single_stranded_RNA_chromosome	SO:0000966
0	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	\N	circular_double_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	SO	43101	SO:0000967	\N	circular_double_stranded_RNA_chromosome	SO:0000967
0	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	\N	insertion_sequence	\N	\N	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	43102	SO:0000973	\N	insertion_sequence	SO:0000973
0	"" []	\N	minicircle_gene	\N	\N	sequence	"" []	SO	43103	SO:0000975	\N	minicircle_gene	SO:0000975
0	"A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke]	\N	cryptic	\N	\N	sequence	"A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke]	SO	43104	SO:0000976	\N	cryptic	SO:0000976
0	"" []	\N	anchor_binding_site	\N	\N	sequence	"" []	SO	43105	SO:0000977	\N	anchor_binding_site	SO:0000977
0	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	\N	template_region	\N	\N	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	43106	SO:0000978	\N	template_region	SO:0000978
0	"A non-protein_coding gene that encodes a guide_RNA." [SO:ma]	\N	gRNA_encoding	\N	\N	sequence	"A non-protein_coding gene that encodes a guide_RNA." [SO:ma]	SO	43107	SO:0000979	\N	gRNA_encoding	SO:0000979
0	"A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]	\N	minicircle	\N	\N	sequence	"A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]	SO	43108	SO:0000980	\N	minicircle	SO:0000980
0	"" []	\N	rho_dependent_bacterial_terminator	\N	\N	sequence	"" []	SO	43109	SO:0000981	\N	rho_dependent_bacterial_terminator	SO:0000981
0	"" []	\N	rho_independent_bacterial_terminator	\N	\N	sequence	"" []	SO	43110	SO:0000982	\N	rho_independent_bacterial_terminator	SO:0000982
0	"" []	\N	strand_attribute	\N	\N	sequence	"" []	SO	43111	SO:0000983	\N	strand_attribute	SO:0000983
0	"" []	\N	single	\N	\N	sequence	"" []	SO	43112	SO:0000984	\N	single	SO:0000984
0	"" []	\N	double	\N	\N	sequence	"" []	SO	43113	SO:0000985	\N	double	SO:0000985
0	"" []	\N	topology_attribute	\N	\N	sequence	"" []	SO	43114	SO:0000986	\N	topology_attribute	SO:0000986
0	"A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]	\N	linear	\N	\N	sequence	"A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]	SO	43115	SO:0000987	\N	linear	SO:0000987
0	"A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]	\N	circular	\N	\N	sequence	"A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]	SO	43116	SO:0000988	\N	circular	SO:0000988
0	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	\N	class_II_RNA	\N	\N	sequence	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	43117	SO:0000989	\N	class_II_RNA	SO:0000989
0	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	\N	class_I_RNA	\N	\N	sequence	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	43118	SO:0000990	\N	class_I_RNA	SO:0000990
0	"" []	\N	genomic_DNA	\N	\N	sequence	"" []	SO	43119	SO:0000991	\N	genomic_DNA	SO:0000991
0	"" []	\N	BAC_cloned_genomic_insert	\N	\N	sequence	"" []	SO	43120	SO:0000992	\N	BAC_cloned_genomic_insert	SO:0000992
0	"" []	\N	consensus	\N	\N	sequence	"" []	SO	43121	SO:0000993	\N	consensus	SO:0000993
0	"" []	\N	consensus_region	\N	\N	sequence	"" []	SO	43122	SO:0000994	\N	consensus_region	SO:0000994
0	"" []	\N	consensus_mRNA	\N	\N	sequence	"" []	SO	43123	SO:0000995	\N	consensus_mRNA	SO:0000995
0	"" []	\N	predicted_gene	\N	\N	sequence	"" []	SO	43124	SO:0000996	\N	predicted_gene	SO:0000996
0	"" []	\N	gene_fragment	\N	\N	sequence	"" []	SO	43125	SO:0000997	\N	gene_fragment	SO:0000997
0	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	\N	recursive_splice_site	\N	\N	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	43126	SO:0000998	\N	recursive_splice_site	SO:0000998
0	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	\N	BAC_end	\N	\N	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	43127	SO:0000999	\N	BAC_end	SO:0000999
0	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SOFA	rRNA_16S	SOFA	\N	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	43128	SO:0001000	\N	rRNA_16S	SO:0001000
0	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SOFA	rRNA_23S	SOFA	\N	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	43129	SO:0001001	\N	rRNA_23S	SO:0001001
0	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SOFA	rRNA_25S	SOFA	\N	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	43130	SO:0001002	\N	rRNA_25S	SO:0001002
0	"A recombination product between the 2 LTR of the same element." [SO:ke]	\N	solo_LTR	\N	\N	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	43131	SO:0001003	\N	solo_LTR	SO:0001003
0	"" []	\N	low_complexity	\N	\N	sequence	"" []	SO	43132	SO:0001004	\N	low_complexity	SO:0001004
0	"" []	\N	low_complexity_region	\N	\N	sequence	"" []	SO	43133	SO:0001005	\N	low_complexity_region	SO:0001005
0	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	\N	prophage	\N	\N	sequence	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	SO	43134	SO:0001006	\N	prophage	SO:0001006
0	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	\N	cryptic_prophage	\N	\N	sequence	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	SO	43135	SO:0001007	\N	cryptic_prophage	SO:0001007
0	"A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]	\N	tetraloop	\N	\N	sequence	"A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]	SO	43136	SO:0001008	\N	tetraloop	SO:0001008
0	"A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	\N	DNA_constraint_sequence	\N	\N	sequence	"A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	SO	43137	SO:0001009	\N	DNA_constraint_sequence	SO:0001009
0	"A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]	\N	i_motif	\N	\N	sequence	"A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]	SO	43138	SO:0001010	\N	i_motif	SO:0001010
0	"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]	\N	PNA_oligo	\N	\N	sequence	"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]	SO	43139	SO:0001011	\N	PNA_oligo	SO:0001011
0	"A DNA sequence with catalytic activity." [SO:cb]	\N	DNAzyme	\N	\N	sequence	"A DNA sequence with catalytic activity." [SO:cb]	SO	43140	SO:0001012	\N	DNAzyme	SO:0001012
0	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	\N	MNP	\N	\N	sequence	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	SO	43141	SO:0001013	\N	MNP	SO:0001013
0	"" []	\N	intron_domain	\N	\N	sequence	"" []	SO	43142	SO:0001014	\N	intron_domain	SO:0001014
0	"A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]	\N	wobble_base_pair	\N	\N	sequence	"A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]	SO	43143	SO:0001015	\N	wobble_base_pair	SO:0001015
0	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	\N	internal_guide_sequence	\N	\N	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	43144	SO:0001016	\N	internal_guide_sequence	SO:0001016
0	"A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke]	\N	silent_mutation	\N	\N	sequence	"A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke]	SO	43145	SO:0001017	\N	silent_mutation	SO:0001017
0	"A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]	\N	epitope	\N	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]	SO	43146	SO:0001018	\N	epitope	SO:0001018
0	"A variation that increases or decreases the copy number of a given region." [SO:ke]	SOFA	copy_number_variation	SOFA	\N	sequence	"A variation that increases or decreases the copy number of a given region." [SO:ke]	SO	43147	SO:0001019	\N	copy_number_variation	SO:0001019
0	"" []	\N	chromosome_breakpoint	\N	\N	sequence	"" []	SO	43148	SO:0001021	\N	chromosome_breakpoint	SO:0001021
0	"The point within a chromosome where an inversion begins or ends." [SO:cb]	\N	inversion_breakpoint	\N	\N	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	43149	SO:0001022	\N	inversion_breakpoint	SO:0001022
0	"An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]	\N	allele	\N	\N	sequence	"An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]	SO	43150	SO:0001023	\N	allele	SO:0001023
0	"A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]	\N	haplotype	\N	\N	sequence	"A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]	SO	43151	SO:0001024	\N	haplotype	SO:0001024
0	"A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]	\N	polymorphic_sequence_variant	\N	\N	sequence	"A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]	SO	43152	SO:0001025	\N	polymorphic_sequence_variant	SO:0001025
0	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	SO	43153	SO:0001026	\N	genome	SO:0001026
0	"A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]	\N	genotype	\N	\N	sequence	"A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]	SO	43154	SO:0001027	\N	genotype	SO:0001027
0	"A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]	\N	diplotype	\N	\N	sequence	"A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]	SO	43155	SO:0001028	\N	diplotype	SO:0001028
0	"" []	\N	direction_attribute	\N	\N	sequence	"" []	SO	43156	SO:0001029	\N	direction_attribute	SO:0001029
0	"Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]	\N	forward	\N	\N	sequence	"Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]	SO	43157	SO:0001030	\N	forward	SO:0001030
0	"Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke]	\N	reverse	\N	\N	sequence	"Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke]	SO	43158	SO:0001031	\N	reverse	SO:0001031
0	"" []	\N	mitochondrial_DNA	\N	\N	sequence	"" []	SO	43159	SO:0001032	\N	mitochondrial_DNA	SO:0001032
0	"" []	\N	chloroplast_DNA	\N	\N	sequence	"" []	SO	43160	SO:0001033	\N	chloroplast_DNA	SO:0001033
0	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	\N	mirtron	\N	\N	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	43161	SO:0001034	\N	mirtron	SO:0001034
0	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	\N	piRNA	\N	\N	sequence	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	SO	43162	SO:0001035	\N	piRNA	SO:0001035
0	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	\N	arginyl_tRNA	\N	\N	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	43163	SO:0001036	\N	arginyl_tRNA	SO:0001036
0	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SOFA	mobile_genetic_element	SOFA	\N	sequence	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SO	43164	SO:0001037	\N	mobile_genetic_element	SO:0001037
0	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"An MGE that is not integrated into the host chromosome." [SO:ke]	SO	43165	SO:0001038	\N	extrachromosomal_mobile_genetic_element	SO:0001038
0	"An MGE that is integrated into the host chromosome." [SO:ke]	SOFA	integrated_mobile_genetic_element	SOFA	\N	sequence	"An MGE that is integrated into the host chromosome." [SO:ke]	SO	43166	SO:0001039	\N	integrated_mobile_genetic_element	SO:0001039
0	"A plasmid sequence that is integrated within the host chromosome." [SO:ke]	\N	integrated_plasmid	\N	\N	sequence	"A plasmid sequence that is integrated within the host chromosome." [SO:ke]	SO	43167	SO:0001040	\N	integrated_plasmid	SO:0001040
0	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	43168	SO:0001041	\N	viral_sequence	SO:0001041
0	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	\N	phage_sequence	\N	\N	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	43169	SO:0001042	\N	phage_sequence	SO:0001042
0	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	\N	attCtn_site	\N	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	43170	SO:0001043	\N	attCtn_site	SO:0001043
0	"A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]	\N	nuclear_mt_pseudogene	\N	\N	sequence	"A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]	SO	43171	SO:0001044	\N	nuclear_mt_pseudogene	SO:0001044
0	"A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]	\N	cointegrated_plasmid	\N	\N	sequence	"A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]	SO	43172	SO:0001045	\N	cointegrated_plasmid	SO:0001045
0	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	\N	IRLinv_site	\N	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	43173	SO:0001046	\N	IRLinv_site	SO:0001046
0	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	\N	IRRinv_site	\N	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	43174	SO:0001047	\N	IRRinv_site	SO:0001047
0	"A region located within an inversion site." [SO:ke]	\N	inversion_site_part	\N	\N	sequence	"A region located within an inversion site." [SO:ke]	SO	43175	SO:0001048	\N	inversion_site_part	SO:0001048
0	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	\N	defective_conjugative_transposon	\N	\N	sequence	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	SO	43176	SO:0001049	\N	defective_conjugative_transposon	SO:0001049
0	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	\N	repeat_fragment	\N	\N	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	43177	SO:0001050	\N	repeat_fragment	SO:0001050
0	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	\N	transposon_fragment	\N	\N	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	43178	SO:0001054	\N	transposon_fragment	SO:0001054
0	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SOFA	transcriptional_cis_regulatory_region	SOFA	\N	sequence	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SO	43179	SO:0001055	\N	transcriptional_cis_regulatory_region	SO:0001055
0	"A regulatory_region that modulates splicing." [SO:ke]	SOFA	splicing_regulatory_region	SOFA	\N	sequence	"A regulatory_region that modulates splicing." [SO:ke]	SO	43180	SO:0001056	\N	splicing_regulatory_region	SO:0001056
0	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	\N	promoter_targeting_sequence	\N	\N	sequence	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	SO	43181	SO:0001058	\N	promoter_targeting_sequence	SO:0001058
0	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SOFA	sequence_alteration	SOFA	\N	sequence	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SO	43182	SO:0001059	\N	sequence_alteration	SO:0001059
0	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	SO	43183	SO:0001060	\N	sequence_variant	SO:0001060
0	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	biosapiens	propeptide_cleavage_site	biosapiens	\N	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	43184	SO:0001061	\N	propeptide_cleavage_site	SO:0001061
0	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	biosapiens	propeptide	biosapiens	\N	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	43185	SO:0001062	\N	propeptide	SO:0001062
0	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens,SOFA	immature_peptide_region	biosapiens,SOFA	\N	sequence	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	SO	43186	SO:0001063	\N	immature_peptide_region	SO:0001063
0	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	active_peptide	biosapiens	\N	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	43187	SO:0001064	\N	active_peptide	SO:0001064
0	"Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	compositionally_biased_region_of_peptide	biosapiens	\N	sequence	"Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]	SO	43188	SO:0001066	\N	compositionally_biased_region_of_peptide	SO:0001066
0	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	\N	sequence	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	SO	43189	SO:0001067	\N	polypeptide_motif	SO:0001067
0	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	biosapiens	polypeptide_repeat	biosapiens	\N	sequence	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	SO	43190	SO:0001068	\N	polypeptide_repeat	SO:0001068
0	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	\N	sequence	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	SO	43191	SO:0001070	\N	polypeptide_structural_region	SO:0001070
0	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	biosapiens	membrane_structure	biosapiens	\N	sequence	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	SO	43192	SO:0001071	\N	membrane_structure	SO:0001071
0	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	biosapiens	extramembrane_polypeptide_region	biosapiens	\N	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	43193	SO:0001072	\N	extramembrane_polypeptide_region	SO:0001072
0	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	biosapiens	cytoplasmic_polypeptide_region	biosapiens	\N	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	43194	SO:0001073	\N	cytoplasmic_polypeptide_region	SO:0001073
0	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	biosapiens	non_cytoplasmic_polypeptide_region	biosapiens	\N	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	43195	SO:0001074	\N	non_cytoplasmic_polypeptide_region	SO:0001074
0	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	biosapiens	intramembrane_polypeptide_region	biosapiens	\N	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	43196	SO:0001075	\N	intramembrane_polypeptide_region	SO:0001075
0	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	biosapiens	membrane_peptide_loop	biosapiens	\N	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	43197	SO:0001076	\N	membrane_peptide_loop	SO:0001076
0	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	biosapiens	transmembrane_polypeptide_region	biosapiens	\N	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	43198	SO:0001077	\N	transmembrane_polypeptide_region	SO:0001077
0	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	\N	sequence	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	SO	43199	SO:0001078	\N	polypeptide_secondary_structure	SO:0001078
0	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	biosapiens	polypeptide_structural_motif	biosapiens	\N	sequence	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	SO	43200	SO:0001079	\N	polypeptide_structural_motif	SO:0001079
0	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	coiled_coil	biosapiens	\N	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	43201	SO:0001080	\N	coiled_coil	SO:0001080
0	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	biosapiens	helix_turn_helix	biosapiens	\N	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	43202	SO:0001081	\N	helix_turn_helix	SO:0001081
0	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	biosapiens	polypeptide_sequencing_information	biosapiens	\N	sequence	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	SO	43203	SO:0001082	\N	polypeptide_sequencing_information	SO:0001082
0	"Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	non_adjacent_residues	biosapiens	\N	sequence	"Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]	SO	43204	SO:0001083	\N	non_adjacent_residues	SO:0001083
0	"The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	non_terminal_residue	biosapiens	\N	sequence	"The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]	SO	43205	SO:0001084	\N	non_terminal_residue	SO:0001084
0	"Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	sequence_conflict	biosapiens	\N	sequence	"Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]	SO	43206	SO:0001085	\N	sequence_conflict	SO:0001085
0	"Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	sequence_uncertainty	biosapiens	\N	sequence	"Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]	SO	43207	SO:0001086	\N	sequence_uncertainty	SO:0001086
0	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	post_translationally_modified_region	biosapiens	\N	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	43208	SO:0001089	\N	post_translationally_modified_region	SO:0001089
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	43209	SO:0001092	\N	polypeptide_metal_contact	SO:0001092
0	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	biosapiens	protein_protein_contact	biosapiens	\N	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	43210	SO:0001093	\N	protein_protein_contact	SO:0001093
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	biosapiens	polypeptide_calcium_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	43211	SO:0001094	\N	polypeptide_calcium_ion_contact_site	SO:0001094
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_cobalt_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	43212	SO:0001095	\N	polypeptide_cobalt_ion_contact_site	SO:0001095
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_copper_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	43213	SO:0001096	\N	polypeptide_copper_ion_contact_site	SO:0001096
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_iron_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	43214	SO:0001097	\N	polypeptide_iron_ion_contact_site	SO:0001097
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_magnesium_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	43215	SO:0001098	\N	polypeptide_magnesium_ion_contact_site	SO:0001098
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_manganese_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	43216	SO:0001099	\N	polypeptide_manganese_ion_contact_site	SO:0001099
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_molybdenum_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	43217	SO:0001100	\N	polypeptide_molybdenum_ion_contact_site	SO:0001100
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	biosapiens	polypeptide_nickel_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	43218	SO:0001101	\N	polypeptide_nickel_ion_contact_site	SO:0001101
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_tungsten_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	43219	SO:0001102	\N	polypeptide_tungsten_ion_contact_site	SO:0001102
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_zinc_ion_contact_site	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	43220	SO:0001103	\N	polypeptide_zinc_ion_contact_site	SO:0001103
0	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	catalytic_residue	biosapiens	\N	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	43221	SO:0001104	\N	catalytic_residue	SO:0001104
0	"Residues which interact with a ligand." [EBIBS:GAR]	biosapiens	polypeptide_ligand_contact	biosapiens	\N	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	43222	SO:0001105	\N	polypeptide_ligand_contact	SO:0001105
0	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_motif	biosapiens	\N	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43223	SO:0001106	\N	asx_motif	SO:0001106
0	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_bulge	biosapiens	\N	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43224	SO:0001107	\N	beta_bulge	SO:0001107
0	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_bulge_loop	biosapiens	\N	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43225	SO:0001108	\N	beta_bulge_loop	SO:0001108
0	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_bulge_loop_five	biosapiens	\N	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43226	SO:0001109	\N	beta_bulge_loop_five	SO:0001109
0	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_bulge_loop_six	biosapiens	\N	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43227	SO:0001110	\N	beta_bulge_loop_six	SO:0001110
0	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	beta_strand	biosapiens	\N	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	43228	SO:0001111	\N	beta_strand	SO:0001111
0	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	antiparallel_beta_strand	biosapiens	\N	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	43229	SO:0001112	\N	antiparallel_beta_strand	SO:0001112
0	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	parallel_beta_strand	biosapiens	\N	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	43230	SO:0001113	\N	parallel_beta_strand	SO:0001113
0	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	biosapiens	peptide_helix	biosapiens	\N	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	43231	SO:0001114	\N	peptide_helix	SO:0001114
0	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	biosapiens	left_handed_peptide_helix	biosapiens	\N	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	43232	SO:0001115	\N	left_handed_peptide_helix	SO:0001115
0	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	biosapiens	right_handed_peptide_helix	biosapiens	\N	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	43233	SO:0001116	\N	right_handed_peptide_helix	SO:0001116
0	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	biosapiens	alpha_helix	biosapiens	\N	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	43234	SO:0001117	\N	alpha_helix	SO:0001117
0	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	biosapiens	pi_helix	biosapiens	\N	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	43235	SO:0001118	\N	pi_helix	SO:0001118
0	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	biosapiens	three_ten_helix	biosapiens	\N	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	43236	SO:0001119	\N	three_ten_helix	SO:0001119
0	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	polypeptide_nest_motif	biosapiens	\N	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43237	SO:0001120	\N	polypeptide_nest_motif	SO:0001120
0	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	polypeptide_nest_left_right_motif	biosapiens	\N	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43238	SO:0001121	\N	polypeptide_nest_left_right_motif	SO:0001121
0	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	polypeptide_nest_right_left_motif	biosapiens	\N	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43239	SO:0001122	\N	polypeptide_nest_right_left_motif	SO:0001122
0	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	schellmann_loop	biosapiens	\N	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43240	SO:0001123	\N	schellmann_loop	SO:0001123
0	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	schellmann_loop_seven	biosapiens	\N	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43241	SO:0001124	\N	schellmann_loop_seven	SO:0001124
0	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	schellmann_loop_six	biosapiens	\N	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43242	SO:0001125	\N	schellmann_loop_six	SO:0001125
0	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	serine_threonine_motif	biosapiens	\N	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43243	SO:0001126	\N	serine_threonine_motif	SO:0001126
0	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	serine_threonine_staple_motif	biosapiens	\N	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43244	SO:0001127	\N	serine_threonine_staple_motif	SO:0001127
0	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	\N	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	43245	SO:0001128	\N	polypeptide_turn_motif	SO:0001128
0	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn_left_handed_type_one	biosapiens	\N	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43246	SO:0001129	\N	asx_turn_left_handed_type_one	SO:0001129
0	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn_left_handed_type_two	biosapiens	\N	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43247	SO:0001130	\N	asx_turn_left_handed_type_two	SO:0001130
0	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn_right_handed_type_two	biosapiens	\N	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43248	SO:0001131	\N	asx_turn_right_handed_type_two	SO:0001131
0	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn_right_handed_type_one	biosapiens	\N	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43249	SO:0001132	\N	asx_turn_right_handed_type_one	SO:0001132
0	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	\N	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43250	SO:0001133	\N	beta_turn	SO:0001133
0	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn_left_handed_type_one	biosapiens	\N	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43251	SO:0001134	\N	beta_turn_left_handed_type_one	SO:0001134
0	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn_left_handed_type_two	biosapiens	\N	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43252	SO:0001135	\N	beta_turn_left_handed_type_two	SO:0001135
0	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn_right_handed_type_one	biosapiens	\N	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43253	SO:0001136	\N	beta_turn_right_handed_type_one	SO:0001136
0	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn_right_handed_type_two	biosapiens	\N	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43254	SO:0001137	\N	beta_turn_right_handed_type_two	SO:0001137
0	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	gamma_turn	biosapiens	\N	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43255	SO:0001138	\N	gamma_turn	SO:0001138
0	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	gamma_turn_classic	biosapiens	\N	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43256	SO:0001139	\N	gamma_turn_classic	SO:0001139
0	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	gamma_turn_inverse	biosapiens	\N	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43257	SO:0001140	\N	gamma_turn_inverse	SO:0001140
0	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	serine_threonine_turn	biosapiens	\N	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43258	SO:0001141	\N	serine_threonine_turn	SO:0001141
0	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	st_turn_left_handed_type_one	biosapiens	\N	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43259	SO:0001142	\N	st_turn_left_handed_type_one	SO:0001142
0	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	st_turn_left_handed_type_two	biosapiens	\N	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43260	SO:0001143	\N	st_turn_left_handed_type_two	SO:0001143
0	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	st_turn_right_handed_type_one	biosapiens	\N	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43261	SO:0001144	\N	st_turn_right_handed_type_one	SO:0001144
0	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	st_turn_right_handed_type_two	biosapiens	\N	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	43262	SO:0001145	\N	st_turn_right_handed_type_two	SO:0001145
0	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	biosapiens	polypeptide_variation_site	biosapiens	\N	sequence	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	SO	43263	SO:0001146	\N	polypeptide_variation_site	SO:0001146
0	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	natural_variant_site	biosapiens	\N	sequence	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	SO	43264	SO:0001147	\N	natural_variant_site	SO:0001147
0	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	mutated_variant_site	biosapiens	\N	sequence	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	SO	43265	SO:0001148	\N	mutated_variant_site	SO:0001148
0	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	alternate_sequence_site	biosapiens	\N	sequence	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	SO	43266	SO:0001149	\N	alternate_sequence_site	SO:0001149
0	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	biosapiens	beta_turn_type_six	biosapiens	\N	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	43267	SO:0001150	\N	beta_turn_type_six	SO:0001150
0	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	biosapiens	beta_turn_type_six_a	biosapiens	\N	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	43268	SO:0001151	\N	beta_turn_type_six_a	SO:0001151
0	"" []	biosapiens	beta_turn_type_six_a_one	biosapiens	\N	sequence	"" []	SO	43269	SO:0001152	\N	beta_turn_type_six_a_one	SO:0001152
0	"" []	biosapiens	beta_turn_type_six_a_two	biosapiens	\N	sequence	"" []	SO	43270	SO:0001153	\N	beta_turn_type_six_a_two	SO:0001153
0	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	biosapiens	beta_turn_type_six_b	biosapiens	\N	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	43271	SO:0001154	\N	beta_turn_type_six_b	SO:0001154
0	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	biosapiens	beta_turn_type_eight	biosapiens	\N	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	43272	SO:0001155	\N	beta_turn_type_eight	SO:0001155
0	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	\N	DRE_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	43273	SO:0001156	\N	DRE_motif	SO:0001156
0	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	\N	DMv4_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	SO	43274	SO:0001157	\N	DMv4_motif	SO:0001157
0	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	\N	E_box_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	43275	SO:0001158	\N	E_box_motif	SO:0001158
0	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	\N	DMv5_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	43276	SO:0001159	\N	DMv5_motif	SO:0001159
0	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	\N	DMv3_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	43277	SO:0001160	\N	DMv3_motif	SO:0001160
0	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	\N	DMv2_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	43278	SO:0001161	\N	DMv2_motif	SO:0001161
0	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	\N	MTE	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	43279	SO:0001162	\N	MTE	SO:0001162
0	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	\N	INR1_motif	\N	\N	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	43280	SO:0001163	\N	INR1_motif	SO:0001163
0	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	\N	DPE1_motif	\N	\N	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	43281	SO:0001164	\N	DPE1_motif	SO:0001164
0	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	\N	DMv1_motif	\N	\N	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	43282	SO:0001165	\N	DMv1_motif	SO:0001165
0	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	\N	GAGA_motif	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	43283	SO:0001166	\N	GAGA_motif	SO:0001166
0	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	\N	NDM2_motif	\N	\N	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	43284	SO:0001167	\N	NDM2_motif	SO:0001167
0	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	\N	NDM3_motif	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	43285	SO:0001168	\N	NDM3_motif	SO:0001168
0	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	\N	ds_RNA_viral_sequence	\N	\N	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	43286	SO:0001169	\N	ds_RNA_viral_sequence	SO:0001169
0	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	\N	polinton	\N	\N	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	43287	SO:0001170	\N	polinton	SO:0001170
0	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	\N	rRNA_21S	\N	\N	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	43288	SO:0001171	\N	rRNA_21S	SO:0001171
0	"A region of a tRNA." [RSC:cb]	\N	tRNA_region	\N	\N	sequence	"A region of a tRNA." [RSC:cb]	SO	43289	SO:0001172	\N	tRNA_region	SO:0001172
0	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	\N	anticodon_loop	\N	\N	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	43290	SO:0001173	\N	anticodon_loop	SO:0001173
0	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	\N	anticodon	\N	\N	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	43291	SO:0001174	\N	anticodon	SO:0001174
0	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	\N	CCA_tail	\N	\N	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	43292	SO:0001175	\N	CCA_tail	SO:0001175
0	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	\N	DHU_loop	\N	\N	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	43293	SO:0001176	\N	DHU_loop	SO:0001176
0	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	\N	T_loop	\N	\N	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	43294	SO:0001177	\N	T_loop	SO:0001177
0	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	\N	pyrrolysine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	43295	SO:0001178	\N	pyrrolysine_tRNA_primary_transcript	SO:0001178
0	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	\N	U3_snoRNA	\N	\N	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	43296	SO:0001179	\N	U3_snoRNA	SO:0001179
0	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	\N	AU_rich_element	\N	\N	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	43297	SO:0001180	\N	AU_rich_element	SO:0001180
0	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	\N	Bruno_response_element	\N	\N	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	43298	SO:0001181	\N	Bruno_response_element	SO:0001181
0	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	\N	iron_responsive_element	\N	\N	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	43299	SO:0001182	\N	iron_responsive_element	SO:0001182
0	"An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]	\N	morpholino_backbone	\N	\N	sequence	"An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]	SO	43300	SO:0001183	\N	morpholino_backbone	SO:0001183
0	"An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]	\N	PNA	\N	\N	sequence	"An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]	SO	43301	SO:0001184	\N	PNA	SO:0001184
0	"An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	\N	enzymatic	\N	\N	sequence	"An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	43302	SO:0001185	\N	enzymatic	SO:0001185
0	"An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]	\N	ribozymic	\N	\N	sequence	"An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]	SO	43303	SO:0001186	\N	ribozymic	SO:0001186
0	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	\N	pseudouridylation_guide_snoRNA	\N	\N	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	43304	SO:0001187	\N	pseudouridylation_guide_snoRNA	SO:0001187
0	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]	\N	LNA	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]	SO	43305	SO:0001188	\N	LNA	SO:0001188
0	"An oligo composed of LNA residues." [RSC:cb]	\N	LNA_oligo	\N	\N	sequence	"An oligo composed of LNA residues." [RSC:cb]	SO	43306	SO:0001189	\N	LNA_oligo	SO:0001189
0	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]	\N	TNA	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]	SO	43307	SO:0001190	\N	TNA	SO:0001190
0	"An oligo composed of TNA residues." [RSC:cb]	\N	TNA_oligo	\N	\N	sequence	"An oligo composed of TNA residues." [RSC:cb]	SO	43308	SO:0001191	\N	TNA_oligo	SO:0001191
0	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]	\N	GNA	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]	SO	43309	SO:0001192	\N	GNA	SO:0001192
0	"An oligo composed of GNA residues." [RSC:cb]	\N	GNA_oligo	\N	\N	sequence	"An oligo composed of GNA residues." [RSC:cb]	SO	43310	SO:0001193	\N	GNA_oligo	SO:0001193
0	"An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]	\N	R_GNA	\N	\N	sequence	"An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]	SO	43311	SO:0001194	\N	R_GNA	SO:0001194
0	"An oligo composed of (R)-GNA residues." [RSC:cb]	\N	R_GNA_oligo	\N	\N	sequence	"An oligo composed of (R)-GNA residues." [RSC:cb]	SO	43312	SO:0001195	\N	R_GNA_oligo	SO:0001195
0	"An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]	\N	S_GNA	\N	\N	sequence	"An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]	SO	43313	SO:0001196	\N	S_GNA	SO:0001196
0	"An oligo composed of (S)-GNA residues." [RSC:cb]	\N	S_GNA_oligo	\N	\N	sequence	"An oligo composed of (S)-GNA residues." [RSC:cb]	SO	43314	SO:0001197	\N	S_GNA_oligo	SO:0001197
0	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	\N	ds_DNA_viral_sequence	\N	\N	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	43315	SO:0001198	\N	ds_DNA_viral_sequence	SO:0001198
0	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	\N	ss_RNA_viral_sequence	\N	\N	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	43316	SO:0001199	\N	ss_RNA_viral_sequence	SO:0001199
0	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	\N	negative_sense_ssRNA_viral_sequence	\N	\N	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	43317	SO:0001200	\N	negative_sense_ssRNA_viral_sequence	SO:0001200
0	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	\N	positive_sense_ssRNA_viral_sequence	\N	\N	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	43318	SO:0001201	\N	positive_sense_ssRNA_viral_sequence	SO:0001201
0	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	\N	ambisense_ssRNA_viral_sequence	\N	\N	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	43319	SO:0001202	\N	ambisense_ssRNA_viral_sequence	SO:0001202
0	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	43320	SO:0001203	\N	RNA_polymerase_promoter	SO:0001203
0	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	Phage_RNA_Polymerase_Promoter	\N	\N	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	43321	SO:0001204	\N	Phage_RNA_Polymerase_Promoter	SO:0001204
0	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	SP6_RNA_Polymerase_Promoter	\N	\N	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	43322	SO:0001205	\N	SP6_RNA_Polymerase_Promoter	SO:0001205
0	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	T3_RNA_Polymerase_Promoter	\N	\N	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	43323	SO:0001206	\N	T3_RNA_Polymerase_Promoter	SO:0001206
0	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	T7_RNA_Polymerase_Promoter	\N	\N	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	43324	SO:0001207	\N	T7_RNA_Polymerase_Promoter	SO:0001207
0	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	\N	five_prime_EST	\N	\N	sequence	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	43325	SO:0001208	\N	five_prime_EST	SO:0001208
0	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	\N	three_prime_EST	\N	\N	sequence	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	43326	SO:0001209	\N	three_prime_EST	SO:0001209
0	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	\N	translational_frameshift	\N	\N	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	43327	SO:0001210	\N	translational_frameshift	SO:0001210
0	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	\N	plus_1_translational_frameshift	\N	\N	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	43328	SO:0001211	\N	plus_1_translational_frameshift	SO:0001211
0	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	\N	plus_2_translational_frameshift	\N	\N	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	43329	SO:0001212	\N	plus_2_translational_frameshift	SO:0001212
0	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	\N	group_III_intron	\N	\N	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	43330	SO:0001213	\N	group_III_intron	SO:0001213
0	"The maximal intersection of exon and UTR." [SO:ke]	SOFA	noncoding_region_of_exon	SOFA	\N	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	43331	SO:0001214	\N	noncoding_region_of_exon	SO:0001214
0	"The region of an exon that encodes for protein sequence." [SO:ke]	SOFA	coding_region_of_exon	SOFA	\N	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	43332	SO:0001215	\N	coding_region_of_exon	SO:0001215
0	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	\N	endonuclease_spliced_intron	\N	\N	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	43333	SO:0001216	\N	endonuclease_spliced_intron	SO:0001216
0	"" []	\N	protein_coding_gene	\N	\N	sequence	"" []	SO	43334	SO:0001217	\N	protein_coding_gene	SO:0001217
0	"An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]	\N	transgenic_insertion	\N	\N	sequence	"An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]	SO	43335	SO:0001218	\N	transgenic_insertion	SO:0001218
0	"" []	\N	retrogene	\N	\N	sequence	"" []	SO	43336	SO:0001219	\N	retrogene	SO:0001219
0	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	\N	silenced_by_RNA_interference	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	SO	43337	SO:0001220	\N	silenced_by_RNA_interference	SO:0001220
0	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	\N	silenced_by_histone_modification	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	SO	43338	SO:0001221	\N	silenced_by_histone_modification	SO:0001221
0	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	\N	silenced_by_histone_methylation	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	43339	SO:0001222	\N	silenced_by_histone_methylation	SO:0001222
0	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	\N	silenced_by_histone_deacetylation	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	43340	SO:0001223	\N	silenced_by_histone_deacetylation	SO:0001223
0	"A gene that is silenced by RNA interference." [SO:xp]	\N	gene_silenced_by_RNA_interference	\N	\N	sequence	"A gene that is silenced by RNA interference." [SO:xp]	SO	43341	SO:0001224	\N	gene_silenced_by_RNA_interference	SO:0001224
0	"A gene that is silenced by histone modification." [SO:xp]	\N	gene_silenced_by_histone_modification	\N	\N	sequence	"A gene that is silenced by histone modification." [SO:xp]	SO	43342	SO:0001225	\N	gene_silenced_by_histone_modification	SO:0001225
0	"A gene that is silenced by histone methylation." [SO:xp]	\N	gene_silenced_by_histone_methylation	\N	\N	sequence	"A gene that is silenced by histone methylation." [SO:xp]	SO	43343	SO:0001226	\N	gene_silenced_by_histone_methylation	SO:0001226
0	"A gene that is silenced by histone deacetylation." [SO:xp]	\N	gene_silenced_by_histone_deacetylation	\N	\N	sequence	"A gene that is silenced by histone deacetylation." [SO:xp]	SO	43344	SO:0001227	\N	gene_silenced_by_histone_deacetylation	SO:0001227
0	"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]	\N	dihydrouridine	\N	\N	sequence	"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]	SO	43345	SO:0001228	\N	dihydrouridine	SO:0001228
0	"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]	\N	pseudouridine	\N	\N	sequence	"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]	SO	43346	SO:0001229	\N	pseudouridine	SO:0001229
0	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	\N	inosine	\N	\N	sequence	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	SO	43347	SO:0001230	\N	inosine	SO:0001230
0	"A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]	\N	seven_methylguanine	\N	\N	sequence	"A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]	SO	43348	SO:0001231	\N	seven_methylguanine	SO:0001231
0	"A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]	\N	ribothymidine	\N	\N	sequence	"A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]	SO	43349	SO:0001232	\N	ribothymidine	SO:0001232
0	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	\N	methylinosine	\N	\N	sequence	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	SO	43350	SO:0001233	\N	methylinosine	SO:0001233
0	"An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb]	\N	mobile	\N	\N	sequence	"An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb]	SO	43351	SO:0001234	\N	mobile	SO:0001234
0	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	\N	sequence	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SO	43352	SO:0001235	\N	replicon	SO:0001235
0	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SOFA	base	SOFA	\N	sequence	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SO	43353	SO:0001236	\N	base	SO:0001236
0	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	SO	43354	SO:0001237	\N	amino_acid	SO:0001237
0	"" []	\N	major_TSS	\N	\N	sequence	"" []	SO	43355	SO:0001238	\N	major_TSS	SO:0001238
0	"" []	\N	minor_TSS	\N	\N	sequence	"" []	SO	43356	SO:0001239	\N	minor_TSS	SO:0001239
0	"The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]	\N	TSS_region	\N	\N	sequence	"The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]	SO	43357	SO:0001240	\N	TSS_region	SO:0001240
0	"" []	\N	encodes_alternate_transcription_start_sites	\N	\N	sequence	"" []	SO	43358	SO:0001241	\N	encodes_alternate_transcription_start_sites	SO:0001241
0	"A part of an miRNA primary_transcript." [SO:ke]	\N	miRNA_primary_transcript_region	\N	\N	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	43359	SO:0001243	\N	miRNA_primary_transcript_region	SO:0001243
0	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	\N	pre_miRNA	\N	\N	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	43360	SO:0001244	\N	pre_miRNA	SO:0001244
0	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	\N	miRNA_stem	\N	\N	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	43361	SO:0001245	\N	miRNA_stem	SO:0001245
0	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	\N	miRNA_loop	\N	\N	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	43362	SO:0001246	\N	miRNA_loop	SO:0001246
0	"An oligo composed of synthetic nucleotides." [SO:ke]	\N	synthetic_oligo	\N	\N	sequence	"An oligo composed of synthetic nucleotides." [SO:ke]	SO	43363	SO:0001247	\N	synthetic_oligo	SO:0001247
0	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	\N	sequence	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SO	43364	SO:0001248	\N	assembly	SO:0001248
0	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	\N	fragment_assembly	\N	\N	sequence	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	SO	43365	SO:0001249	\N	fragment_assembly	SO:0001249
0	"A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]	\N	fingerprint_map	\N	\N	sequence	"A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]	SO	43366	SO:0001250	\N	fingerprint_map	SO:0001250
0	"An STS map is a physical map organized by the unique STS landmarks." [SO:ke]	\N	STS_map	\N	\N	sequence	"An STS map is a physical map organized by the unique STS landmarks." [SO:ke]	SO	43367	SO:0001251	\N	STS_map	SO:0001251
0	"A radiation hybrid map is a physical map." [SO:ke]	\N	RH_map	\N	\N	sequence	"A radiation hybrid map is a physical map." [SO:ke]	SO	43368	SO:0001252	\N	RH_map	SO:0001252
0	"A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]	\N	sonicate_fragment	\N	\N	sequence	"A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]	SO	43369	SO:0001253	\N	sonicate_fragment	SO:0001253
0	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	\N	polyploid	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	43370	SO:0001254	\N	polyploid	SO:0001254
0	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	\N	autopolyploid	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	43371	SO:0001255	\N	autopolyploid	SO:0001255
0	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	\N	allopolyploid	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	43372	SO:0001256	\N	allopolyploid	SO:0001256
0	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	\N	homing_endonuclease_binding_site	\N	\N	sequence	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	SO	43373	SO:0001257	\N	homing_endonuclease_binding_site	SO:0001257
0	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	\N	octamer_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	43374	SO:0001258	\N	octamer_motif	SO:0001258
0	"A chromosome originating in an apicoplast." [SO:xp]	\N	apicoplast_chromosome	\N	\N	sequence	"A chromosome originating in an apicoplast." [SO:xp]	SO	43375	SO:0001259	\N	apicoplast_chromosome	SO:0001259
0	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A collection of discontinuous sequences." [SO:ke]	SO	43376	SO:0001260	\N	sequence_collection	SO:0001260
0	"A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]	\N	overlapping_feature_set	\N	\N	sequence	"A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]	SO	43377	SO:0001261	\N	overlapping_feature_set	SO:0001261
0	"A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]	\N	overlapping_EST_set	\N	\N	sequence	"A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]	SO	43378	SO:0001262	\N	overlapping_EST_set	SO:0001262
0	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	43379	SO:0001263	\N	ncRNA_gene	SO:0001263
0	"" []	\N	gRNA_gene	\N	\N	sequence	"" []	SO	43380	SO:0001264	\N	gRNA_gene	SO:0001264
0	"" []	\N	miRNA_gene	\N	\N	sequence	"" []	SO	43381	SO:0001265	\N	miRNA_gene	SO:0001265
0	"" []	\N	scRNA_gene	\N	\N	sequence	"" []	SO	43382	SO:0001266	\N	scRNA_gene	SO:0001266
0	"" []	\N	snoRNA_gene	\N	\N	sequence	"" []	SO	43383	SO:0001267	\N	snoRNA_gene	SO:0001267
0	"" []	\N	snRNA_gene	\N	\N	sequence	"" []	SO	43384	SO:0001268	\N	snRNA_gene	SO:0001268
0	"" []	\N	SRP_RNA_gene	\N	\N	sequence	"" []	SO	43385	SO:0001269	\N	SRP_RNA_gene	SO:0001269
0	"" []	\N	stRNA_gene	\N	\N	sequence	"" []	SO	43386	SO:0001270	\N	stRNA_gene	SO:0001270
0	"" []	\N	tmRNA_gene	\N	\N	sequence	"" []	SO	43387	SO:0001271	\N	tmRNA_gene	SO:0001271
0	"" []	\N	tRNA_gene	\N	\N	sequence	"" []	SO	43388	SO:0001272	\N	tRNA_gene	SO:0001272
0	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	SO	43389	SO:0001273	\N	modified_adenosine	SO:0001273
0	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	\N	modified_inosine	\N	\N	sequence	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	SO	43390	SO:0001274	\N	modified_inosine	SO:0001274
0	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	SO	43391	SO:0001275	\N	modified_cytidine	SO:0001275
0	"" []	\N	modified_guanosine	\N	\N	sequence	"" []	SO	43392	SO:0001276	\N	modified_guanosine	SO:0001276
0	"" []	\N	modified_uridine	\N	\N	sequence	"" []	SO	43393	SO:0001277	\N	modified_uridine	SO:0001277
0	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	\N	one_methylinosine	\N	\N	sequence	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	43394	SO:0001278	\N	one_methylinosine	SO:0001278
0	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	\N	one_two_prime_O_dimethylinosine	\N	\N	sequence	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	43395	SO:0001279	\N	one_two_prime_O_dimethylinosine	SO:0001279
0	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	\N	two_prime_O_methylinosine	\N	\N	sequence	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	43396	SO:0001280	\N	two_prime_O_methylinosine	SO:0001280
0	"3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	three_methylcytidine	\N	\N	sequence	"3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43397	SO:0001281	\N	three_methylcytidine	SO:0001281
0	"5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	five_methylcytidine	\N	\N	sequence	"5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43398	SO:0001282	\N	five_methylcytidine	SO:0001282
0	"2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	two_prime_O_methylcytidine	\N	\N	sequence	"2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43399	SO:0001283	\N	two_prime_O_methylcytidine	SO:0001283
0	"2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	two_thiocytidine	\N	\N	sequence	"2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43400	SO:0001284	\N	two_thiocytidine	SO:0001284
0	"N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	N4_acetylcytidine	\N	\N	sequence	"N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43401	SO:0001285	\N	N4_acetylcytidine	SO:0001285
0	"5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	five_formylcytidine	\N	\N	sequence	"5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43402	SO:0001286	\N	five_formylcytidine	SO:0001286
0	"5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	five_two_prime_O_dimethylcytidine	\N	\N	sequence	"5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43403	SO:0001287	\N	five_two_prime_O_dimethylcytidine	SO:0001287
0	"N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	N4_acetyl_2_prime_O_methylcytidine	\N	\N	sequence	"N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43404	SO:0001288	\N	N4_acetyl_2_prime_O_methylcytidine	SO:0001288
0	"Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	lysidine	\N	\N	sequence	"Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43405	SO:0001289	\N	lysidine	SO:0001289
0	"N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	N4_methylcytidine	\N	\N	sequence	"N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43406	SO:0001290	\N	N4_methylcytidine	SO:0001290
0	"N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	N4_2_prime_O_dimethylcytidine	\N	\N	sequence	"N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43407	SO:0001291	\N	N4_2_prime_O_dimethylcytidine	SO:0001291
0	"5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	five_hydroxymethylcytidine	\N	\N	sequence	"5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43408	SO:0001292	\N	five_hydroxymethylcytidine	SO:0001292
0	"5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	five_formyl_two_prime_O_methylcytidine	\N	\N	sequence	"5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43409	SO:0001293	\N	five_formyl_two_prime_O_methylcytidine	SO:0001293
0	"N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	\N	N4_N4_2_prime_O_trimethylcytidine	\N	\N	sequence	"N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	43410	SO:0001294	\N	N4_N4_2_prime_O_trimethylcytidine	SO:0001294
0	"1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	one_methyladenosine	\N	\N	sequence	"1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43411	SO:0001295	\N	one_methyladenosine	SO:0001295
0	"2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	two_methyladenosine	\N	\N	sequence	"2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43412	SO:0001296	\N	two_methyladenosine	SO:0001296
0	"N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_methyladenosine	\N	\N	sequence	"N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43413	SO:0001297	\N	N6_methyladenosine	SO:0001297
0	"2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	two_prime_O_methyladenosine	\N	\N	sequence	"2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43414	SO:0001298	\N	two_prime_O_methyladenosine	SO:0001298
0	"2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	two_methylthio_N6_methyladenosine	\N	\N	sequence	"2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43415	SO:0001299	\N	two_methylthio_N6_methyladenosine	SO:0001299
0	"N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_isopentenyladenosine	\N	\N	sequence	"N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43416	SO:0001300	\N	N6_isopentenyladenosine	SO:0001300
0	"2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	two_methylthio_N6_isopentenyladenosine	\N	\N	sequence	"2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43417	SO:0001301	\N	two_methylthio_N6_isopentenyladenosine	SO:0001301
0	"N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_cis_hydroxyisopentenyl_adenosine	\N	\N	sequence	"N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43418	SO:0001302	\N	N6_cis_hydroxyisopentenyl_adenosine	SO:0001302
0	"2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	\N	\N	sequence	"2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43419	SO:0001303	\N	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	SO:0001303
0	"N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_glycinylcarbamoyladenosine	\N	\N	sequence	"N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43420	SO:0001304	\N	N6_glycinylcarbamoyladenosine	SO:0001304
0	"N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_threonylcarbamoyladenosine	\N	\N	sequence	"N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43421	SO:0001305	\N	N6_threonylcarbamoyladenosine	SO:0001305
0	"2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	two_methylthio_N6_threonyl_carbamoyladenosine	\N	\N	sequence	"2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43422	SO:0001306	\N	two_methylthio_N6_threonyl_carbamoyladenosine	SO:0001306
0	"N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_methyl_N6_threonylcarbamoyladenosine	\N	\N	sequence	"N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43423	SO:0001307	\N	N6_methyl_N6_threonylcarbamoyladenosine	SO:0001307
0	"N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_hydroxynorvalylcarbamoyladenosine	\N	\N	sequence	"N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43424	SO:0001308	\N	N6_hydroxynorvalylcarbamoyladenosine	SO:0001308
0	"2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	\N	\N	sequence	"2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43425	SO:0001309	\N	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	SO:0001309
0	"2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	two_prime_O_ribosyladenosine_phosphate	\N	\N	sequence	"2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43426	SO:0001310	\N	two_prime_O_ribosyladenosine_phosphate	SO:0001310
0	"N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_N6_dimethyladenosine	\N	\N	sequence	"N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43427	SO:0001311	\N	N6_N6_dimethyladenosine	SO:0001311
0	"N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_2_prime_O_dimethyladenosine	\N	\N	sequence	"N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43428	SO:0001312	\N	N6_2_prime_O_dimethyladenosine	SO:0001312
0	"N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_N6_2_prime_O_trimethyladenosine	\N	\N	sequence	"N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43429	SO:0001313	\N	N6_N6_2_prime_O_trimethyladenosine	SO:0001313
0	"1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	one_two_prime_O_dimethyladenosine	\N	\N	sequence	"1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43430	SO:0001314	\N	one_two_prime_O_dimethyladenosine	SO:0001314
0	"N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	\N	N6_acetyladenosine	\N	\N	sequence	"N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	43431	SO:0001315	\N	N6_acetyladenosine	SO:0001315
0	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_deazaguanosine	\N	\N	sequence	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	SO	43432	SO:0001316	\N	seven_deazaguanosine	SO:0001316
0	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	\N	queuosine	\N	\N	sequence	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	43433	SO:0001317	\N	queuosine	SO:0001317
0	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	\N	epoxyqueuosine	\N	\N	sequence	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	43434	SO:0001318	\N	epoxyqueuosine	SO:0001318
0	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	\N	galactosyl_queuosine	\N	\N	sequence	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	43435	SO:0001319	\N	galactosyl_queuosine	SO:0001319
0	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	\N	mannosyl_queuosine	\N	\N	sequence	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	43436	SO:0001320	\N	mannosyl_queuosine	SO:0001320
0	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_cyano_seven_deazaguanosine	\N	\N	sequence	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	43437	SO:0001321	\N	seven_cyano_seven_deazaguanosine	SO:0001321
0	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_aminomethyl_seven_deazaguanosine	\N	\N	sequence	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	43438	SO:0001322	\N	seven_aminomethyl_seven_deazaguanosine	SO:0001322
0	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	\N	archaeosine	\N	\N	sequence	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	43439	SO:0001323	\N	archaeosine	SO:0001323
0	"1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	one_methylguanosine	\N	\N	sequence	"1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43440	SO:0001324	\N	one_methylguanosine	SO:0001324
0	"N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	N2_methylguanosine	\N	\N	sequence	"N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43441	SO:0001325	\N	N2_methylguanosine	SO:0001325
0	"7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	seven_methylguanosine	\N	\N	sequence	"7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43442	SO:0001326	\N	seven_methylguanosine	SO:0001326
0	"2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	two_prime_O_methylguanosine	\N	\N	sequence	"2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43443	SO:0001327	\N	two_prime_O_methylguanosine	SO:0001327
0	"N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	N2_N2_dimethylguanosine	\N	\N	sequence	"N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43444	SO:0001328	\N	N2_N2_dimethylguanosine	SO:0001328
0	"N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	N2_2_prime_O_dimethylguanosine	\N	\N	sequence	"N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43445	SO:0001329	\N	N2_2_prime_O_dimethylguanosine	SO:0001329
0	"N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	N2_N2_2_prime_O_trimethylguanosine	\N	\N	sequence	"N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43446	SO:0001330	\N	N2_N2_2_prime_O_trimethylguanosine	SO:0001330
0	"2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	two_prime_O_ribosylguanosine_phosphate	\N	\N	sequence	"2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43447	SO:0001331	\N	two_prime_O_ribosylguanosine_phosphate	SO:0001331
0	"Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	wybutosine	\N	\N	sequence	"Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43448	SO:0001332	\N	wybutosine	SO:0001332
0	"Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	peroxywybutosine	\N	\N	sequence	"Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43449	SO:0001333	\N	peroxywybutosine	SO:0001333
0	"Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	hydroxywybutosine	\N	\N	sequence	"Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43450	SO:0001334	\N	hydroxywybutosine	SO:0001334
0	"Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	undermodified_hydroxywybutosine	\N	\N	sequence	"Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43451	SO:0001335	\N	undermodified_hydroxywybutosine	SO:0001335
0	"Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	wyosine	\N	\N	sequence	"Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43452	SO:0001336	\N	wyosine	SO:0001336
0	"Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	methylwyosine	\N	\N	sequence	"Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43453	SO:0001337	\N	methylwyosine	SO:0001337
0	"N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	N2_7_dimethylguanosine	\N	\N	sequence	"N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43454	SO:0001338	\N	N2_7_dimethylguanosine	SO:0001338
0	"N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	N2_N2_7_trimethylguanosine	\N	\N	sequence	"N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43455	SO:0001339	\N	N2_N2_7_trimethylguanosine	SO:0001339
0	"1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	one_two_prime_O_dimethylguanosine	\N	\N	sequence	"1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43456	SO:0001340	\N	one_two_prime_O_dimethylguanosine	SO:0001340
0	"4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	four_demethylwyosine	\N	\N	sequence	"4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43457	SO:0001341	\N	four_demethylwyosine	SO:0001341
0	"Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	isowyosine	\N	\N	sequence	"Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43458	SO:0001342	\N	isowyosine	SO:0001342
0	"N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	\N	N2_7_2prirme_O_trimethylguanosine	\N	\N	sequence	"N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43459	SO:0001343	\N	N2_7_2prirme_O_trimethylguanosine	SO:0001343
0	"5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methyluridine	\N	\N	sequence	"5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43460	SO:0001344	\N	five_methyluridine	SO:0001344
0	"2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	two_prime_O_methyluridine	\N	\N	sequence	"2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43461	SO:0001345	\N	two_prime_O_methyluridine	SO:0001345
0	"5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_two_prime_O_dimethyluridine	\N	\N	sequence	"5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43462	SO:0001346	\N	five_two_prime_O_dimethyluridine	SO:0001346
0	"1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	one_methylpseudouridine	\N	\N	sequence	"1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43463	SO:0001347	\N	one_methylpseudouridine	SO:0001347
0	"2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	two_prime_O_methylpseudouridine	\N	\N	sequence	"2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43464	SO:0001348	\N	two_prime_O_methylpseudouridine	SO:0001348
0	"2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	two_thiouridine	\N	\N	sequence	"2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43465	SO:0001349	\N	two_thiouridine	SO:0001349
0	"4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	four_thiouridine	\N	\N	sequence	"4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43466	SO:0001350	\N	four_thiouridine	SO:0001350
0	"5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methyl_2_thiouridine	\N	\N	sequence	"5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43467	SO:0001351	\N	five_methyl_2_thiouridine	SO:0001351
0	"2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	two_thio_two_prime_O_methyluridine	\N	\N	sequence	"2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43468	SO:0001352	\N	two_thio_two_prime_O_methyluridine	SO:0001352
0	"3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	three_three_amino_three_carboxypropyl_uridine	\N	\N	sequence	"3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43469	SO:0001353	\N	three_three_amino_three_carboxypropyl_uridine	SO:0001353
0	"5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_hydroxyuridine	\N	\N	sequence	"5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43470	SO:0001354	\N	five_hydroxyuridine	SO:0001354
0	"5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methoxyuridine	\N	\N	sequence	"5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43471	SO:0001355	\N	five_methoxyuridine	SO:0001355
0	"Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	uridine_five_oxyacetic_acid	\N	\N	sequence	"Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43472	SO:0001356	\N	uridine_five_oxyacetic_acid	SO:0001356
0	"Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	uridine_five_oxyacetic_acid_methyl_ester	\N	\N	sequence	"Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43473	SO:0001357	\N	uridine_five_oxyacetic_acid_methyl_ester	SO:0001357
0	"5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_carboxyhydroxymethyl_uridine	\N	\N	sequence	"5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43474	SO:0001358	\N	five_carboxyhydroxymethyl_uridine	SO:0001358
0	"5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_carboxyhydroxymethyl_uridine_methyl_ester	\N	\N	sequence	"5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43475	SO:0001359	\N	five_carboxyhydroxymethyl_uridine_methyl_ester	SO:0001359
0	"Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methoxycarbonylmethyluridine	\N	\N	sequence	"Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43476	SO:0001360	\N	five_methoxycarbonylmethyluridine	SO:0001360
0	"Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methoxycarbonylmethyl_two_prime_O_methyluridine	\N	\N	sequence	"Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43477	SO:0001361	\N	five_methoxycarbonylmethyl_two_prime_O_methyluridine	SO:0001361
0	"5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methoxycarbonylmethyl_two_thiouridine	\N	\N	sequence	"5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43478	SO:0001362	\N	five_methoxycarbonylmethyl_two_thiouridine	SO:0001362
0	"5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_aminomethyl_two_thiouridine	\N	\N	sequence	"5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43479	SO:0001363	\N	five_aminomethyl_two_thiouridine	SO:0001363
0	"5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methylaminomethyluridine	\N	\N	sequence	"5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43480	SO:0001364	\N	five_methylaminomethyluridine	SO:0001364
0	"5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methylaminomethyl_two_thiouridine	\N	\N	sequence	"5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43481	SO:0001365	\N	five_methylaminomethyl_two_thiouridine	SO:0001365
0	"5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methylaminomethyl_two_selenouridine	\N	\N	sequence	"5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43482	SO:0001366	\N	five_methylaminomethyl_two_selenouridine	SO:0001366
0	"5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_carbamoylmethyluridine	\N	\N	sequence	"5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43483	SO:0001367	\N	five_carbamoylmethyluridine	SO:0001367
0	"5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_carbamoylmethyl_two_prime_O_methyluridine	\N	\N	sequence	"5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43484	SO:0001368	\N	five_carbamoylmethyl_two_prime_O_methyluridine	SO:0001368
0	"5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_carboxymethylaminomethyluridine	\N	\N	sequence	"5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43485	SO:0001369	\N	five_carboxymethylaminomethyluridine	SO:0001369
0	"5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_carboxymethylaminomethyl_two_prime_O_methyluridine	\N	\N	sequence	"5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43486	SO:0001370	\N	five_carboxymethylaminomethyl_two_prime_O_methyluridine	SO:0001370
0	"5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_carboxymethylaminomethyl_two_thiouridine	\N	\N	sequence	"5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43487	SO:0001371	\N	five_carboxymethylaminomethyl_two_thiouridine	SO:0001371
0	"3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	three_methyluridine	\N	\N	sequence	"3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43488	SO:0001372	\N	three_methyluridine	SO:0001372
0	"1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	\N	\N	sequence	"1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43489	SO:0001373	\N	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	SO:0001373
0	"5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_carboxymethyluridine	\N	\N	sequence	"5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43490	SO:0001374	\N	five_carboxymethyluridine	SO:0001374
0	"3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	three_two_prime_O_dimethyluridine	\N	\N	sequence	"3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43491	SO:0001375	\N	three_two_prime_O_dimethyluridine	SO:0001375
0	"5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_methyldihydrouridine	\N	\N	sequence	"5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43492	SO:0001376	\N	five_methyldihydrouridine	SO:0001376
0	"3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	three_methylpseudouridine	\N	\N	sequence	"3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43493	SO:0001377	\N	three_methylpseudouridine	SO:0001377
0	"5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_taurinomethyluridine	\N	\N	sequence	"5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43494	SO:0001378	\N	five_taurinomethyluridine	SO:0001378
0	"5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_taurinomethyl_two_thiouridine	\N	\N	sequence	"5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43495	SO:0001379	\N	five_taurinomethyl_two_thiouridine	SO:0001379
0	"5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_isopentenylaminomethyl_uridine	\N	\N	sequence	"5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43496	SO:0001380	\N	five_isopentenylaminomethyl_uridine	SO:0001380
0	"5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_isopentenylaminomethyl_two_thiouridine	\N	\N	sequence	"5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43497	SO:0001381	\N	five_isopentenylaminomethyl_two_thiouridine	SO:0001381
0	"5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	\N	five_isopentenylaminomethyl_two_prime_O_methyluridine	\N	\N	sequence	"5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	43498	SO:0001382	\N	five_isopentenylaminomethyl_two_prime_O_methyluridine	SO:0001382
0	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]	\N	histone_binding_site	\N	\N	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]	SO	43499	SO:0001383	\N	histone_binding_site	SO:0001383
0	"" []	\N	CDS_fragment	\N	\N	sequence	"" []	SO	43500	SO:0001384	\N	CDS_fragment	SO:0001384
0	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified amino acid feature." [SO:ke]	SO	43501	SO:0001385	\N	modified_amino_acid_feature	SO:0001385
0	"A post translationally modified glycine amino acid feature." [SO:ke]	\N	modified_glycine	\N	\N	sequence	"A post translationally modified glycine amino acid feature." [SO:ke]	SO	43502	SO:0001386	\N	modified_glycine	SO:0001386
0	"A post translationally modified alanine amino acid feature." [SO:ke]	\N	modified_L_alanine	\N	\N	sequence	"A post translationally modified alanine amino acid feature." [SO:ke]	SO	43503	SO:0001387	\N	modified_L_alanine	SO:0001387
0	"A post translationally modified asparagine amino acid feature." [SO:ke]	\N	modified_L_asparagine	\N	\N	sequence	"A post translationally modified asparagine amino acid feature." [SO:ke]	SO	43504	SO:0001388	\N	modified_L_asparagine	SO:0001388
0	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	\N	modified_L_aspartic_acid	\N	\N	sequence	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	SO	43505	SO:0001389	\N	modified_L_aspartic_acid	SO:0001389
0	"A post translationally modified cysteine amino acid feature." [SO:ke]	\N	modified_L_cysteine	\N	\N	sequence	"A post translationally modified cysteine amino acid feature." [SO:ke]	SO	43506	SO:0001390	\N	modified_L_cysteine	SO:0001390
0	"" []	\N	modified_L_glutamic_acid	\N	\N	sequence	"" []	SO	43507	SO:0001391	\N	modified_L_glutamic_acid	SO:0001391
0	"A post translationally modified threonine amino acid feature." [SO:ke]	\N	modified_L_threonine	\N	\N	sequence	"A post translationally modified threonine amino acid feature." [SO:ke]	SO	43508	SO:0001392	\N	modified_L_threonine	SO:0001392
0	"A post translationally modified tryptophan amino acid feature." [SO:ke]	\N	modified_L_tryptophan	\N	\N	sequence	"A post translationally modified tryptophan amino acid feature." [SO:ke]	SO	43509	SO:0001393	\N	modified_L_tryptophan	SO:0001393
0	"A post translationally modified glutamine amino acid feature." [SO:ke]	\N	modified_L_glutamine	\N	\N	sequence	"A post translationally modified glutamine amino acid feature." [SO:ke]	SO	43510	SO:0001394	\N	modified_L_glutamine	SO:0001394
0	"A post translationally modified methionine amino acid feature." [SO:ke]	\N	modified_L_methionine	\N	\N	sequence	"A post translationally modified methionine amino acid feature." [SO:ke]	SO	43511	SO:0001395	\N	modified_L_methionine	SO:0001395
0	"A post translationally modified isoleucine amino acid feature." [SO:ke]	\N	modified_L_isoleucine	\N	\N	sequence	"A post translationally modified isoleucine amino acid feature." [SO:ke]	SO	43512	SO:0001396	\N	modified_L_isoleucine	SO:0001396
0	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	\N	modified_L_phenylalanine	\N	\N	sequence	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	SO	43513	SO:0001397	\N	modified_L_phenylalanine	SO:0001397
0	"A post translationally modified histidine amino acid feature." [SO:ke]	\N	modified_L_histidine	\N	\N	sequence	"A post translationally modified histidine amino acid feature." [SO:ke]	SO	43514	SO:0001398	\N	modified_L_histidine	SO:0001398
0	"A post translationally modified serine amino acid feature." [SO:ke]	\N	modified_L_serine	\N	\N	sequence	"A post translationally modified serine amino acid feature." [SO:ke]	SO	43515	SO:0001399	\N	modified_L_serine	SO:0001399
0	"A post translationally modified lysine amino acid feature." [SO:ke]	\N	modified_L_lysine	\N	\N	sequence	"A post translationally modified lysine amino acid feature." [SO:ke]	SO	43516	SO:0001400	\N	modified_L_lysine	SO:0001400
0	"A post translationally modified leucine amino acid feature." [SO:ke]	\N	modified_L_leucine	\N	\N	sequence	"A post translationally modified leucine amino acid feature." [SO:ke]	SO	43517	SO:0001401	\N	modified_L_leucine	SO:0001401
0	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	\N	modified_L_selenocysteine	\N	\N	sequence	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	SO	43518	SO:0001402	\N	modified_L_selenocysteine	SO:0001402
0	"A post translationally modified valine amino acid feature." [SO:ke]	\N	modified_L_valine	\N	\N	sequence	"A post translationally modified valine amino acid feature." [SO:ke]	SO	43519	SO:0001403	\N	modified_L_valine	SO:0001403
0	"A post translationally modified proline amino acid feature." [SO:ke]	\N	modified_L_proline	\N	\N	sequence	"A post translationally modified proline amino acid feature." [SO:ke]	SO	43520	SO:0001404	\N	modified_L_proline	SO:0001404
0	"A post translationally modified tyrosine amino acid feature." [SO:ke]	\N	modified_L_tyrosine	\N	\N	sequence	"A post translationally modified tyrosine amino acid feature." [SO:ke]	SO	43521	SO:0001405	\N	modified_L_tyrosine	SO:0001405
0	"A post translationally modified arginine amino acid feature." [SO:ke]	\N	modified_L_arginine	\N	\N	sequence	"A post translationally modified arginine amino acid feature." [SO:ke]	SO	43522	SO:0001406	\N	modified_L_arginine	SO:0001406
0	"An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke]	\N	peptidyl	\N	\N	sequence	"An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke]	SO	43523	SO:0001407	\N	peptidyl	SO:0001407
0	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	\N	cleaved_for_gpi_anchor_region	\N	\N	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	43524	SO:0001408	\N	cleaved_for_gpi_anchor_region	SO:0001408
0	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	\N	sequence	"A region which is intended for use in an experiment." [SO:cb]	SO	43525	SO:0001409	\N	biomaterial_region	SO:0001409
0	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	\N	sequence	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SO	43526	SO:0001410	\N	experimental_feature	SO:0001410
0	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	\N	sequence	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SO	43527	SO:0001411	\N	biological_region	SO:0001411
0	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	SOFA	topologically_defined_region	SOFA	\N	sequence	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	SO	43528	SO:0001412	\N	topologically_defined_region	SO:0001412
0	"The point within a chromosome where a translocation begins or ends." [SO:cb]	\N	translocation_breakpoint	\N	\N	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	43529	SO:0001413	\N	translocation_breakpoint	SO:0001413
0	"The point within a chromosome where a insertion begins or ends." [SO:cb]	\N	insertion_breakpoint	\N	\N	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	43530	SO:0001414	\N	insertion_breakpoint	SO:0001414
0	"The point within a chromosome where a deletion begins or ends." [SO:cb]	\N	deletion_breakpoint	\N	\N	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	43531	SO:0001415	\N	deletion_breakpoint	SO:0001415
0	"A flanking region located five prime of a specific region." [SO:chado]	\N	five_prime_flanking_region	\N	\N	sequence	"A flanking region located five prime of a specific region." [SO:chado]	SO	43532	SO:0001416	\N	five_prime_flanking_region	SO:0001416
0	"A flanking region located three prime of a specific region." [SO:chado]	\N	three_prime_flanking_region	\N	\N	sequence	"A flanking region located three prime of a specific region." [SO:chado]	SO	43533	SO:0001417	\N	three_prime_flanking_region	SO:0001417
0	"An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]	\N	transcribed_fragment	\N	\N	sequence	"An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]	SO	43534	SO:0001418	\N	transcribed_fragment	SO:0001418
0	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SOFA	cis_splice_site	SOFA	\N	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	43535	SO:0001419	\N	cis_splice_site	SO:0001419
0	"Primary transcript region bordering trans-splice junction." [SO:ke]	SOFA	trans_splice_site	SOFA	\N	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	43536	SO:0001420	\N	trans_splice_site	SO:0001420
0	"The boundary between an intron and an exon." [SO:ke]	\N	splice_junction	\N	\N	sequence	"The boundary between an intron and an exon." [SO:ke]	SO	43537	SO:0001421	\N	splice_junction	SO:0001421
0	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	\N	conformational_switch	\N	\N	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	43538	SO:0001422	\N	conformational_switch	SO:0001422
0	"A read produced by the dye terminator method of sequencing." [SO:ke]	\N	dye_terminator_read	\N	\N	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	43539	SO:0001423	\N	dye_terminator_read	SO:0001423
0	"A read produced by pyrosequencing technology." [SO:ke]	\N	pyrosequenced_read	\N	\N	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	43540	SO:0001424	\N	pyrosequenced_read	SO:0001424
0	"A read produced by ligation based sequencing technologies." [SO:ke]	\N	ligation_based_read	\N	\N	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	43541	SO:0001425	\N	ligation_based_read	SO:0001425
0	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	\N	polymerase_synthesis_read	\N	\N	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	43542	SO:0001426	\N	polymerase_synthesis_read	SO:0001426
0	"A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]	\N	cis_regulatory_frameshift_element	\N	\N	sequence	"A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]	SO	43543	SO:0001427	\N	cis_regulatory_frameshift_element	SO:0001427
0	"A sequence assembly derived from expressed sequences." [SO:ke]	\N	expressed_sequence_assembly	\N	\N	sequence	"A sequence assembly derived from expressed sequences." [SO:ke]	SO	43544	SO:0001428	\N	expressed_sequence_assembly	SO:0001428
0	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	\N	DNA_binding_site	\N	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	SO	43545	SO:0001429	\N	DNA_binding_site	SO:0001429
0	"A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]	\N	cryptic_gene	\N	\N	sequence	"A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]	SO	43546	SO:0001431	\N	cryptic_gene	SO:0001431
0	"A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]	\N	three_prime_RACE_clone	\N	\N	sequence	"A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]	SO	43547	SO:0001433	\N	three_prime_RACE_clone	SO:0001433
0	"A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]	\N	cassette_pseudogene	\N	\N	sequence	"A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]	SO	43548	SO:0001434	\N	cassette_pseudogene	SO:0001434
0	"" []	\N	alanine	\N	\N	sequence	"" []	SO	43549	SO:0001435	\N	alanine	SO:0001435
0	"" []	\N	valine	\N	\N	sequence	"" []	SO	43550	SO:0001436	\N	valine	SO:0001436
0	"" []	\N	leucine	\N	\N	sequence	"" []	SO	43551	SO:0001437	\N	leucine	SO:0001437
0	"" []	\N	isoleucine	\N	\N	sequence	"" []	SO	43552	SO:0001438	\N	isoleucine	SO:0001438
0	"" []	\N	proline	\N	\N	sequence	"" []	SO	43553	SO:0001439	\N	proline	SO:0001439
0	"" []	\N	tryptophan	\N	\N	sequence	"" []	SO	43554	SO:0001440	\N	tryptophan	SO:0001440
0	"" []	\N	phenylalanine	\N	\N	sequence	"" []	SO	43555	SO:0001441	\N	phenylalanine	SO:0001441
0	"" []	\N	methionine	\N	\N	sequence	"" []	SO	43556	SO:0001442	\N	methionine	SO:0001442
0	"" []	\N	glycine	\N	\N	sequence	"" []	SO	43557	SO:0001443	\N	glycine	SO:0001443
0	"" []	\N	serine	\N	\N	sequence	"" []	SO	43558	SO:0001444	\N	serine	SO:0001444
0	"" []	\N	threonine	\N	\N	sequence	"" []	SO	43559	SO:0001445	\N	threonine	SO:0001445
0	"" []	\N	tyrosine	\N	\N	sequence	"" []	SO	43560	SO:0001446	\N	tyrosine	SO:0001446
0	"" []	\N	cysteine	\N	\N	sequence	"" []	SO	43561	SO:0001447	\N	cysteine	SO:0001447
0	"" []	\N	glutamine	\N	\N	sequence	"" []	SO	43562	SO:0001448	\N	glutamine	SO:0001448
0	"" []	\N	asparagine	\N	\N	sequence	"" []	SO	43563	SO:0001449	\N	asparagine	SO:0001449
0	"" []	\N	lysine	\N	\N	sequence	"" []	SO	43564	SO:0001450	\N	lysine	SO:0001450
0	"" []	\N	arginine	\N	\N	sequence	"" []	SO	43565	SO:0001451	\N	arginine	SO:0001451
0	"" []	\N	histidine	\N	\N	sequence	"" []	SO	43566	SO:0001452	\N	histidine	SO:0001452
0	"" []	\N	aspartic_acid	\N	\N	sequence	"" []	SO	43567	SO:0001453	\N	aspartic_acid	SO:0001453
0	"" []	\N	glutamic_acid	\N	\N	sequence	"" []	SO	43568	SO:0001454	\N	glutamic_acid	SO:0001454
0	"" []	\N	selenocysteine	\N	\N	sequence	"" []	SO	43569	SO:0001455	\N	selenocysteine	SO:0001455
0	"" []	\N	pyrrolysine	\N	\N	sequence	"" []	SO	43570	SO:0001456	\N	pyrrolysine	SO:0001456
0	"A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]	\N	transcribed_cluster	\N	\N	sequence	"A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]	SO	43571	SO:0001457	\N	transcribed_cluster	SO:0001457
0	"A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]	\N	unigene_cluster	\N	\N	sequence	"A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]	SO	43572	SO:0001458	\N	unigene_cluster	SO:0001458
0	"Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]	\N	CRISPR	\N	\N	sequence	"Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]	SO	43573	SO:0001459	\N	CRISPR	SO:0001459
0	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	insulator_binding_site	\N	\N	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	43574	SO:0001460	\N	insulator_binding_site	SO:0001460
0	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	enhancer_binding_site	\N	\N	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	43575	SO:0001461	\N	enhancer_binding_site	SO:0001461
0	"A collection of contigs." [SO:ke]	\N	contig_collection	\N	\N	sequence	"A collection of contigs." [SO:ke]	SO	43576	SO:0001462	\N	contig_collection	SO:0001462
0	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	\N	lincRNA	\N	\N	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	43577	SO:0001463	\N	lincRNA	SO:0001463
0	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	\N	UST	\N	\N	sequence	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	SO	43578	SO:0001464	\N	UST	SO:0001464
0	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	\N	three_prime_UST	\N	\N	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	43579	SO:0001465	\N	three_prime_UST	SO:0001465
0	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	\N	five_prime_UST	\N	\N	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	43580	SO:0001466	\N	five_prime_UST	SO:0001466
0	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	\N	RST	\N	\N	sequence	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	43581	SO:0001467	\N	RST	SO:0001467
0	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	\N	three_prime_RST	\N	\N	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	43582	SO:0001468	\N	three_prime_RST	SO:0001468
0	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	\N	five_prime_RST	\N	\N	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	43583	SO:0001469	\N	five_prime_RST	SO:0001469
0	"A match against an UST sequence." [SO:nlw]	\N	UST_match	\N	\N	sequence	"A match against an UST sequence." [SO:nlw]	SO	43584	SO:0001470	\N	UST_match	SO:0001470
0	"A match against an RST sequence." [SO:nlw]	\N	RST_match	\N	\N	sequence	"A match against an RST sequence." [SO:nlw]	SO	43585	SO:0001471	\N	RST_match	SO:0001471
0	"A nucleotide match to a primer sequence." [SO:nlw]	\N	primer_match	\N	\N	sequence	"A nucleotide match to a primer sequence." [SO:nlw]	SO	43586	SO:0001472	\N	primer_match	SO:0001472
0	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	\N	miRNA_antiguide	\N	\N	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	43587	SO:0001473	\N	miRNA_antiguide	SO:0001473
0	"The boundary between the spliced leader and the first exon of the mRNA." [SO:ke]	\N	trans_splice_junction	\N	\N	sequence	"The boundary between the spliced leader and the first exon of the mRNA." [SO:ke]	SO	43588	SO:0001474	\N	trans_splice_junction	SO:0001474
0	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	\N	outron	\N	\N	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	43589	SO:0001475	\N	outron	SO:0001475
0	"A plasmid that occurs naturally." [SO:xp]	\N	natural_plasmid	\N	\N	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	43590	SO:0001476	\N	natural_plasmid	SO:0001476
0	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	\N	gene_trap_construct	\N	\N	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	43591	SO:0001477	\N	gene_trap_construct	SO:0001477
0	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	\N	promoter_trap_construct	\N	\N	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	43592	SO:0001478	\N	promoter_trap_construct	SO:0001478
0	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	\N	enhancer_trap_construct	\N	\N	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	43593	SO:0001479	\N	enhancer_trap_construct	SO:0001479
0	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	\N	PAC_end	\N	\N	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	43594	SO:0001480	\N	PAC_end	SO:0001480
0	"RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]	\N	RAPD	\N	\N	sequence	"RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]	SO	43595	SO:0001481	\N	RAPD	SO:0001481
0	"" []	\N	shadow_enhancer	\N	\N	sequence	"" []	SO	43596	SO:0001482	\N	shadow_enhancer	SO:0001482
0	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SOFA	SNV	SOFA	\N	sequence	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SO	43597	SO:0001483	\N	SNV	SO:0001483
0	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	\N	X_element_combinatorial_repeat	\N	\N	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	43598	SO:0001484	\N	X_element_combinatorial_repeat	SO:0001484
0	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	\N	Y_prime_element	\N	\N	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	43599	SO:0001485	\N	Y_prime_element	SO:0001485
0	"The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]	\N	standard_draft	\N	\N	sequence	"The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]	SO	43600	SO:0001486	\N	standard_draft	SO:0001486
0	"The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]	\N	high_quality_draft	\N	\N	sequence	"The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]	SO	43601	SO:0001487	\N	high_quality_draft	SO:0001487
0	"The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]	\N	improved_high_quality_draft	\N	\N	sequence	"The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]	SO	43602	SO:0001488	\N	improved_high_quality_draft	SO:0001488
0	"The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]	\N	annotation_directed_improved_draft	\N	\N	sequence	"The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]	SO	43603	SO:0001489	\N	annotation_directed_improved_draft	SO:0001489
0	"The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]	\N	noncontiguous_finished	\N	\N	sequence	"The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]	SO	43604	SO:0001490	\N	noncontiguous_finished	SO:0001490
0	"The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]	\N	finished_genome	\N	\N	sequence	"The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]	SO	43605	SO:0001491	\N	finished_genome	SO:0001491
0	"A regulatory region that is part of an intron." [SO:ke]	\N	intronic_regulatory_region	\N	\N	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	43606	SO:0001492	\N	intronic_regulatory_region	SO:0001492
0	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	\N	centromere_DNA_Element_I	\N	\N	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	43607	SO:0001493	\N	centromere_DNA_Element_I	SO:0001493
0	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	\N	centromere_DNA_Element_II	\N	\N	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	43608	SO:0001494	\N	centromere_DNA_Element_II	SO:0001494
0	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	\N	centromere_DNA_Element_III	\N	\N	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	43609	SO:0001495	\N	centromere_DNA_Element_III	SO:0001495
0	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	\N	telomeric_repeat	\N	\N	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	43610	SO:0001496	\N	telomeric_repeat	SO:0001496
0	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	\N	X_element	\N	\N	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	43611	SO:0001497	\N	X_element	SO:0001497
0	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	\N	YAC_end	\N	\N	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	43612	SO:0001498	\N	YAC_end	SO:0001498
0	"The status of whole genome sequence." [DOI:10.1126]	\N	whole_genome_sequence_status	\N	\N	sequence	"The status of whole genome sequence." [DOI:10.1126]	SO	43613	SO:0001499	\N	whole_genome_sequence_status	SO:0001499
0	"A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]	\N	heritable_phenotypic_marker	\N	\N	sequence	"A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]	SO	43614	SO:0001500	\N	heritable_phenotypic_marker	SO:0001500
0	"A collection of peptide sequences." [BBOP:nlw]	\N	peptide_collection	\N	\N	sequence	"A collection of peptide sequences." [BBOP:nlw]	SO	43615	SO:0001501	\N	peptide_collection	SO:0001501
0	"An experimental feature with high sequence identity to another sequence." [SO:ke]	\N	high_identity_region	\N	\N	sequence	"An experimental feature with high sequence identity to another sequence." [SO:ke]	SO	43616	SO:0001502	\N	high_identity_region	SO:0001502
0	"A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]	\N	processed_transcript	\N	\N	sequence	"A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]	SO	43617	SO:0001503	\N	processed_transcript	SO:0001503
0	"A chromosome variation derived from an event during meiosis." [SO:ke]	\N	assortment_derived_variation	\N	\N	sequence	"A chromosome variation derived from an event during meiosis." [SO:ke]	SO	43618	SO:0001504	\N	assortment_derived_variation	SO:0001504
0	"A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke]	\N	reference_genome	\N	\N	sequence	"A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke]	SO	43619	SO:0001505	\N	reference_genome	SO:0001505
0	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	SO	43620	SO:0001506	\N	variant_genome	SO:0001506
0	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A collection of one or more sequences of an individual." [SO:ke]	SO	43621	SO:0001507	\N	variant_collection	SO:0001507
0	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	43622	SO:0001508	\N	alteration_attribute	SO:0001508
0	"" []	\N	chromosomal_variation_attribute	\N	\N	sequence	"" []	SO	43623	SO:0001509	\N	chromosomal_variation_attribute	SO:0001509
0	"" []	\N	intrachromosomal	\N	\N	sequence	"" []	SO	43624	SO:0001510	\N	intrachromosomal	SO:0001510
0	"" []	\N	interchromosomal	\N	\N	sequence	"" []	SO	43625	SO:0001511	\N	interchromosomal	SO:0001511
0	"A quality of a chromosomal insertion,." [SO:ke]	\N	insertion_attribute	\N	\N	sequence	"A quality of a chromosomal insertion,." [SO:ke]	SO	43626	SO:0001512	\N	insertion_attribute	SO:0001512
0	"" []	\N	tandem	\N	\N	sequence	"" []	SO	43627	SO:0001513	\N	tandem	SO:0001513
0	"A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]	\N	direct	\N	\N	sequence	"A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]	SO	43628	SO:0001514	\N	direct	SO:0001514
0	"A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]	\N	inverted	\N	\N	sequence	"A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]	SO	43629	SO:0001515	\N	inverted	SO:0001515
0	"The quality of a duplication where the new region exists independently of the original." [SO:ke]	\N	free	\N	\N	sequence	"The quality of a duplication where the new region exists independently of the original." [SO:ke]	SO	43630	SO:0001516	\N	free	SO:0001516
0	"" []	\N	inversion_attribute	\N	\N	sequence	"" []	SO	43631	SO:0001517	\N	inversion_attribute	SO:0001517
0	"" []	\N	pericentric	\N	\N	sequence	"" []	SO	43632	SO:0001518	\N	pericentric	SO:0001518
0	"" []	\N	paracentric	\N	\N	sequence	"" []	SO	43633	SO:0001519	\N	paracentric	SO:0001519
0	"" []	\N	translocaton_attribute	\N	\N	sequence	"" []	SO	43634	SO:0001520	\N	translocaton_attribute	SO:0001520
0	"" []	\N	reciprocal	\N	\N	sequence	"" []	SO	43635	SO:0001521	\N	reciprocal	SO:0001521
0	"" []	\N	insertional	\N	\N	sequence	"" []	SO	43636	SO:0001522	\N	insertional	SO:0001522
0	"" []	\N	duplication_attribute	\N	\N	sequence	"" []	SO	43637	SO:0001523	\N	duplication_attribute	SO:0001523
0	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"" []	SO	43638	SO:0001524	\N	chromosomally_aberrant_genome	SO:0001524
0	"A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]	\N	assembly_error_correction	\N	\N	sequence	"A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]	SO	43639	SO:0001525	\N	assembly_error_correction	SO:0001525
0	"A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]	\N	base_call_error_correction	\N	\N	sequence	"A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]	SO	43640	SO:0001526	\N	base_call_error_correction	SO:0001526
0	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	SOFA	peptide_localization_signal	SOFA	\N	sequence	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	SO	43641	SO:0001527	\N	peptide_localization_signal	SO:0001527
0	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	\N	nuclear_localization_signal	\N	\N	sequence	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	SO	43642	SO:0001528	\N	nuclear_localization_signal	SO:0001528
0	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	\N	endosomal_localization_signal	\N	\N	sequence	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	SO	43643	SO:0001529	\N	endosomal_localization_signal	SO:0001529
0	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	\N	lysosomal_localization_signal	\N	\N	sequence	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	SO	43644	SO:0001530	\N	lysosomal_localization_signal	SO:0001530
0	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	\N	nuclear_export_signal	\N	\N	sequence	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	SO	43645	SO:0001531	\N	nuclear_export_signal	SO:0001531
0	"A region recognized by a recombinase." [SO:ke]	\N	recombination_signal_sequence	\N	\N	sequence	"A region recognized by a recombinase." [SO:ke]	SO	43646	SO:0001532	\N	recombination_signal_sequence	SO:0001532
0	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	\N	cryptic_splice_site	\N	\N	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	43647	SO:0001533	\N	cryptic_splice_site	SO:0001533
0	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	\N	nuclear_rim_localization_signal	\N	\N	sequence	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	SO	43648	SO:0001534	\N	nuclear_rim_localization_signal	SO:0001534
0	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	\N	p_element	\N	\N	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	43649	SO:0001535	\N	p_element	SO:0001535
0	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	SO	43650	SO:0001536	\N	functional_variant	SO:0001536
0	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that changes one or more sequence features." [SO:ke]	SO	43651	SO:0001537	\N	structural_variant	SO:0001537
0	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	SO	43652	SO:0001538	\N	transcript_function_variant	SO:0001538
0	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	SO	43653	SO:0001539	\N	translational_product_function_variant	SO:0001539
0	"A sequence variant which alters the level of a transcript." [SO:ke]	\N	level_of_transcript_variant	\N	\N	sequence	"A sequence variant which alters the level of a transcript." [SO:ke]	SO	43654	SO:0001540	\N	level_of_transcript_variant	SO:0001540
0	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	\N	decreased_transcript_level_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	43655	SO:0001541	\N	decreased_transcript_level_variant	SO:0001541
0	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	\N	increased_transcript_level_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	43656	SO:0001542	\N	increased_transcript_level_variant	SO:0001542
0	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_processing_variant	\N	\N	sequence	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	SO	43657	SO:0001543	\N	transcript_processing_variant	SO:0001543
0	"A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]	\N	editing_variant	\N	\N	sequence	"A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]	SO	43658	SO:0001544	\N	editing_variant	SO:0001544
0	"A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]	\N	polyadenylation_variant	\N	\N	sequence	"A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]	SO	43659	SO:0001545	\N	polyadenylation_variant	SO:0001545
0	"A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_stability_variant	\N	\N	sequence	"A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]	SO	43660	SO:0001546	\N	transcript_stability_variant	SO:0001546
0	"A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]	\N	decreased_transcript_stability_variant	\N	\N	sequence	"A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]	SO	43661	SO:0001547	\N	decreased_transcript_stability_variant	SO:0001547
0	"A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]	\N	increased_transcript_stability_variant	\N	\N	sequence	"A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]	SO	43662	SO:0001548	\N	increased_transcript_stability_variant	SO:0001548
0	"A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]	\N	transcription_variant	\N	\N	sequence	"A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]	SO	43663	SO:0001549	\N	transcription_variant	SO:0001549
0	"A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]	\N	rate_of_transcription_variant	\N	\N	sequence	"A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]	SO	43664	SO:0001550	\N	rate_of_transcription_variant	SO:0001550
0	"A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]	\N	increased_transcription_rate_variant	\N	\N	sequence	"A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	43665	SO:0001551	\N	increased_transcription_rate_variant	SO:0001551
0	"A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]	\N	decreased_transcription_rate_variant	\N	\N	sequence	"A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	43666	SO:0001552	\N	decreased_transcription_rate_variant	SO:0001552
0	"A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]	\N	translational_product_level_variant	\N	\N	sequence	"A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]	SO	43667	SO:0001553	\N	translational_product_level_variant	SO:0001553
0	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	\N	polypeptide_function_variant	\N	\N	sequence	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	SO	43668	SO:0001554	\N	polypeptide_function_variant	SO:0001554
0	"A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]	\N	decreased_translational_product_level	\N	\N	sequence	"A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]	SO	43669	SO:0001555	\N	decreased_translational_product_level	SO:0001555
0	"A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]	\N	increased_translational_product_level	\N	\N	sequence	"A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]	SO	43670	SO:0001556	\N	increased_translational_product_level	SO:0001556
0	"A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]	\N	polypeptide_gain_of_function_variant	\N	\N	sequence	"A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]	SO	43671	SO:0001557	\N	polypeptide_gain_of_function_variant	SO:0001557
0	"A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]	\N	polypeptide_localization_variant	\N	\N	sequence	"A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]	SO	43672	SO:0001558	\N	polypeptide_localization_variant	SO:0001558
0	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	\N	polypeptide_loss_of_function_variant	\N	\N	sequence	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	SO	43673	SO:0001559	\N	polypeptide_loss_of_function_variant	SO:0001559
0	"A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]	\N	inactive_ligand_binding_site	\N	\N	sequence	"A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]	SO	43674	SO:0001560	\N	inactive_ligand_binding_site	SO:0001560
0	"A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]	\N	polypeptide_partial_loss_of_function	\N	\N	sequence	"A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]	SO	43675	SO:0001561	\N	polypeptide_partial_loss_of_function	SO:0001561
0	"A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]	\N	polypeptide_post_translational_processing_variant	\N	\N	sequence	"A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]	SO	43676	SO:0001562	\N	polypeptide_post_translational_processing_variant	SO:0001562
0	"A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]	\N	copy_number_change	\N	\N	sequence	"A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]	SO	43677	SO:0001563	\N	copy_number_change	SO:0001563
0	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant where the structure of the gene is changed." [SO:ke]	SO	43678	SO:0001564	\N	gene_variant	SO:0001564
0	"A sequence variant whereby a two genes have become joined." [SO:ke]	\N	gene_fusion	\N	\N	sequence	"A sequence variant whereby a two genes have become joined." [SO:ke]	SO	43679	SO:0001565	\N	gene_fusion	SO:0001565
0	"A sequence variant located within a regulatory region." [SO:ke]	\N	regulatory_region_variant	\N	\N	sequence	"A sequence variant located within a regulatory region." [SO:ke]	SO	43680	SO:0001566	\N	regulatory_region_variant	SO:0001566
0	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	\N	stop_retained_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	43681	SO:0001567	\N	stop_retained_variant	SO:0001567
0	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant that changes the process of splicing." [SO:ke]	SO	43682	SO:0001568	\N	splicing_variant	SO:0001568
0	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	cryptic_splice_site_variant	\N	\N	sequence	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	43683	SO:0001569	\N	cryptic_splice_site_variant	SO:0001569
0	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	\N	cryptic_splice_acceptor	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	SO	43684	SO:0001570	\N	cryptic_splice_acceptor	SO:0001570
0	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	\N	cryptic_splice_donor	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	SO	43685	SO:0001571	\N	cryptic_splice_donor	SO:0001571
0	"A sequence variant whereby an exon is lost from the transcript." [SO:ke]	\N	exon_loss_variant	\N	\N	sequence	"A sequence variant whereby an exon is lost from the transcript." [SO:ke]	SO	43686	SO:0001572	\N	exon_loss_variant	SO:0001572
0	"A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	intron_gain	\N	\N	sequence	"A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	43687	SO:0001573	\N	intron_gain	SO:0001573
0	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	\N	splice_acceptor_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	43688	SO:0001574	\N	splice_acceptor_variant	SO:0001574
0	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	\N	splice_donor_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	43689	SO:0001575	\N	splice_donor_variant	SO:0001575
0	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes the structure of the transcript." [SO:ke]	SO	43690	SO:0001576	\N	transcript_variant	SO:0001576
0	"A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]	\N	complex_transcript_variant	\N	\N	sequence	"A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]	SO	43691	SO:0001577	\N	complex_transcript_variant	SO:0001577
0	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	\N	stop_lost	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	43692	SO:0001578	\N	stop_lost	SO:0001578
0	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	43693	SO:0001580	\N	coding_sequence_variant	SO:0001580
0	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	\N	initiator_codon_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	43694	SO:0001582	\N	initiator_codon_variant	SO:0001582
0	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	\N	missense_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	43695	SO:0001583	\N	missense_variant	SO:0001583
0	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	\N	conservative_missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	43696	SO:0001585	\N	conservative_missense_variant	SO:0001585
0	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	\N	non_conservative_missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	43697	SO:0001586	\N	non_conservative_missense_variant	SO:0001586
0	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	\N	stop_gained	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	43698	SO:0001587	\N	stop_gained	SO:0001587
0	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	\N	frameshift_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	43699	SO:0001589	\N	frameshift_variant	SO:0001589
0	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	\N	terminator_codon_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	43700	SO:0001590	\N	terminator_codon_variant	SO:0001590
0	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	\N	frame_restoring_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	43701	SO:0001591	\N	frame_restoring_variant	SO:0001591
0	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	\N	minus_1_frameshift_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	43702	SO:0001592	\N	minus_1_frameshift_variant	SO:0001592
0	"" []	\N	minus_2_frameshift_variant	\N	\N	sequence	"" []	SO	43703	SO:0001593	\N	minus_2_frameshift_variant	SO:0001593
0	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	\N	plus_1_frameshift_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	43704	SO:0001594	\N	plus_1_frameshift_variant	SO:0001594
0	"" []	\N	plus_2_frameshift_variant	\N	\N	sequence	"" []	SO	43705	SO:0001595	\N	plus_2_frameshift_variant	SO:0001595
0	"A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]	\N	transcript_secondary_structure_variant	\N	\N	sequence	"A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]	SO	43706	SO:0001596	\N	transcript_secondary_structure_variant	SO:0001596
0	"A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]	\N	compensatory_transcript_secondary_structure_variant	\N	\N	sequence	"A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]	SO	43707	SO:0001597	\N	compensatory_transcript_secondary_structure_variant	SO:0001597
0	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	SO	43708	SO:0001598	\N	translational_product_structure_variant	SO:0001598
0	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	\N	3D_polypeptide_structure_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	43709	SO:0001599	\N	3D_polypeptide_structure_variant	SO:0001599
0	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	\N	complex_3D_structural_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	43710	SO:0001600	\N	complex_3D_structural_variant	SO:0001600
0	"A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]	\N	conformational_change_variant	\N	\N	sequence	"A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]	SO	43711	SO:0001601	\N	conformational_change_variant	SO:0001601
0	"" []	\N	complex_change_of_translational_product_variant	\N	\N	sequence	"" []	SO	43712	SO:0001602	\N	complex_change_of_translational_product_variant	SO:0001602
0	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	SO	43713	SO:0001603	\N	polypeptide_sequence_variant	SO:0001603
0	"A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]	\N	amino_acid_deletion	\N	\N	sequence	"A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]	SO	43714	SO:0001604	\N	amino_acid_deletion	SO:0001604
0	"A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]	\N	amino_acid_insertion	\N	\N	sequence	"A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]	SO	43715	SO:0001605	\N	amino_acid_insertion	SO:0001605
0	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	\N	amino_acid_substitution	\N	\N	sequence	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	SO	43716	SO:0001606	\N	amino_acid_substitution	SO:0001606
0	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	\N	conservative_amino_acid_substitution	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	SO	43717	SO:0001607	\N	conservative_amino_acid_substitution	SO:0001607
0	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	\N	non_conservative_amino_acid_substitution	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	SO	43718	SO:0001608	\N	non_conservative_amino_acid_substitution	SO:0001608
0	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	\N	elongated_polypeptide	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	SO	43719	SO:0001609	\N	elongated_polypeptide	SO:0001609
0	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	\N	elongated_polypeptide_C_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	43720	SO:0001610	\N	elongated_polypeptide_C_terminal	SO:0001610
0	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	\N	elongated_polypeptide_N_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	43721	SO:0001611	\N	elongated_polypeptide_N_terminal	SO:0001611
0	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	\N	elongated_in_frame_polypeptide_C_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	43722	SO:0001612	\N	elongated_in_frame_polypeptide_C_terminal	SO:0001612
0	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	\N	elongated_out_of_frame_polypeptide_C_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	43723	SO:0001613	\N	elongated_out_of_frame_polypeptide_C_terminal	SO:0001613
0	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	\N	elongated_in_frame_polypeptide_N_terminal_elongation	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	43724	SO:0001614	\N	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001614
0	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	\N	elongated_out_of_frame_polypeptide_N_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	43725	SO:0001615	\N	elongated_out_of_frame_polypeptide_N_terminal	SO:0001615
0	"A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]	\N	polypeptide_fusion	\N	\N	sequence	"A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]	SO	43726	SO:0001616	\N	polypeptide_fusion	SO:0001616
0	"A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]	\N	polypeptide_truncation	\N	\N	sequence	"A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]	SO	43727	SO:0001617	\N	polypeptide_truncation	SO:0001617
0	"A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]	\N	inactive_catalytic_site	\N	\N	sequence	"A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]	SO	43728	SO:0001618	\N	inactive_catalytic_site	SO:0001618
0	"A transcript variant of a non coding RNA gene." [SO:ke]	\N	non_coding_transcript_variant	\N	\N	sequence	"A transcript variant of a non coding RNA gene." [SO:ke]	SO	43729	SO:0001619	\N	non_coding_transcript_variant	SO:0001619
0	"A transcript variant located with the sequence of the mature miRNA." [SO:ke]	\N	mature_miRNA_variant	\N	\N	sequence	"A transcript variant located with the sequence of the mature miRNA." [SO:ke]	SO	43730	SO:0001620	\N	mature_miRNA_variant	SO:0001620
0	"A variant in a transcript that is the target of NMD." [SO:ke]	\N	NMD_transcript_variant	\N	\N	sequence	"A variant in a transcript that is the target of NMD." [SO:ke]	SO	43731	SO:0001621	\N	NMD_transcript_variant	SO:0001621
0	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	43732	SO:0001622	\N	UTR_variant	SO:0001622
0	"A UTR variant of the 5' UTR." [SO:ke]	\N	5_prime_UTR_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	43733	SO:0001623	\N	5_prime_UTR_variant	SO:0001623
0	"A UTR variant of the 3' UTR." [SO:ke]	\N	3_prime_UTR_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	43734	SO:0001624	\N	3_prime_UTR_variant	SO:0001624
0	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	\N	incomplete_terminal_codon_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	43735	SO:0001626	\N	incomplete_terminal_codon_variant	SO:0001626
0	"A transcript variant occurring within an intron." [SO:ke]	\N	intron_variant	\N	\N	sequence	"A transcript variant occurring within an intron." [SO:ke]	SO	43736	SO:0001627	\N	intron_variant	SO:0001627
0	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A sequence variant located in the intergenic region, between genes." [SO:ke]	SO	43737	SO:0001628	\N	intergenic_variant	SO:0001628
0	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	\N	splice_site_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	43738	SO:0001629	\N	splice_site_variant	SO:0001629
0	"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]	\N	splice_region_variant	\N	\N	sequence	"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]	SO	43739	SO:0001630	\N	splice_region_variant	SO:0001630
0	"A sequence variant located 5' of a gene." [SO:ke]	\N	upstream_gene_variant	\N	\N	sequence	"A sequence variant located 5' of a gene." [SO:ke]	SO	43740	SO:0001631	\N	upstream_gene_variant	SO:0001631
0	"A sequence variant located 3' of a gene." [SO:ke]	\N	downstream_gene_variant	\N	\N	sequence	"A sequence variant located 3' of a gene." [SO:ke]	SO	43741	SO:0001632	\N	downstream_gene_variant	SO:0001632
0	"A sequence variant located within 5 KB of the end of a gene." [SO:ke]	\N	5KB_downstream_variant	\N	\N	sequence	"A sequence variant located within 5 KB of the end of a gene." [SO:ke]	SO	43742	SO:0001633	\N	5KB_downstream_variant	SO:0001633
0	"A sequence variant located within a half KB of the end of a gene." [SO:ke]	\N	500B_downstream_variant	\N	\N	sequence	"A sequence variant located within a half KB of the end of a gene." [SO:ke]	SO	43743	SO:0001634	\N	500B_downstream_variant	SO:0001634
0	"A sequence variant located within 5KB 5' of a gene." [SO:ke]	\N	5KB_upstream_variant	\N	\N	sequence	"A sequence variant located within 5KB 5' of a gene." [SO:ke]	SO	43744	SO:0001635	\N	5KB_upstream_variant	SO:0001635
0	"A sequence variant located within 2KB 5' of a gene." [SO:ke]	\N	2KB_upstream_variant	\N	\N	sequence	"A sequence variant located within 2KB 5' of a gene." [SO:ke]	SO	43745	SO:0001636	\N	2KB_upstream_variant	SO:0001636
0	"A gene that encodes for ribosomal RNA." [SO:ke]	\N	rRNA_gene	\N	\N	sequence	"A gene that encodes for ribosomal RNA." [SO:ke]	SO	43746	SO:0001637	\N	rRNA_gene	SO:0001637
0	"A gene that encodes for an piwi associated RNA." [SO:ke]	\N	piRNA_gene	\N	\N	sequence	"A gene that encodes for an piwi associated RNA." [SO:ke]	SO	43747	SO:0001638	\N	piRNA_gene	SO:0001638
0	"A gene that encodes an RNase P RNA." [SO:ke]	\N	RNase_P_RNA_gene	\N	\N	sequence	"A gene that encodes an RNase P RNA." [SO:ke]	SO	43748	SO:0001639	\N	RNase_P_RNA_gene	SO:0001639
0	"A gene that encodes a RNase_MRP_RNA." [SO:ke]	\N	RNase_MRP_RNA_gene	\N	\N	sequence	"A gene that encodes a RNase_MRP_RNA." [SO:ke]	SO	43749	SO:0001640	\N	RNase_MRP_RNA_gene	SO:0001640
0	"A gene that encodes large intervening non-coding RNA." [SO:ke]	\N	lincRNA_gene	\N	\N	sequence	"A gene that encodes large intervening non-coding RNA." [SO:ke]	SO	43750	SO:0001641	\N	lincRNA_gene	SO:0001641
0	"A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill]	\N	mathematically_defined_repeat	\N	\N	sequence	"A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill]	SO	43751	SO:0001642	\N	mathematically_defined_repeat	SO:0001642
0	"A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]	\N	telomerase_RNA_gene	\N	\N	sequence	"A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]	SO	43752	SO:0001643	\N	telomerase_RNA_gene	SO:0001643
0	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	\N	targeting_vector	\N	\N	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	43753	SO:0001644	\N	targeting_vector	SO:0001644
0	"A measurable sequence feature that varies within a population." [SO:db]	\N	genetic_marker	\N	\N	sequence	"A measurable sequence feature that varies within a population." [SO:db]	SO	43754	SO:0001645	\N	genetic_marker	SO:0001645
0	"A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]	\N	DArT_marker	\N	\N	sequence	"A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]	SO	43755	SO:0001646	\N	DArT_marker	SO:0001646
0	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SOFA	kozak_sequence	SOFA	\N	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	43756	SO:0001647	\N	kozak_sequence	SO:0001647
0	"A transposon that is disrupted by the insertion of another element." [SO:ke]	\N	nested_transposon	\N	\N	sequence	"A transposon that is disrupted by the insertion of another element." [SO:ke]	SO	43757	SO:0001648	\N	nested_transposon	SO:0001648
0	"A repeat that is disrupted by the insertion of another element." [SO:ke]	\N	nested_repeat	\N	\N	sequence	"A repeat that is disrupted by the insertion of another element." [SO:ke]	SO	43758	SO:0001649	\N	nested_repeat	SO:0001649
0	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	43759	SO:0001650	\N	inframe_variant	SO:0001650
0	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	\N	retinoic_acid_responsive_element	\N	\N	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	43760	SO:0001653	\N	retinoic_acid_responsive_element	SO:0001653
0	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SOFA	nucleotide_to_protein_binding_site	SOFA	\N	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	43761	SO:0001654	\N	nucleotide_to_protein_binding_site	SO:0001654
0	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	\N	nucleotide_binding_site	\N	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	SO	43762	SO:0001655	\N	nucleotide_binding_site	SO:0001655
0	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	\N	metal_binding_site	\N	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	SO	43763	SO:0001656	\N	metal_binding_site	SO:0001656
0	"A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]	\N	ligand_binding_site	\N	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]	SO	43764	SO:0001657	\N	ligand_binding_site	SO:0001657
0	"An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]	\N	nested_tandem_repeat	\N	\N	sequence	"An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]	SO	43765	SO:0001658	\N	nested_tandem_repeat	SO:0001658
0	"" []	\N	promoter_element	\N	\N	sequence	"" []	SO	43766	SO:0001659	\N	promoter_element	SO:0001659
0	"" []	\N	core_promoter_element	\N	\N	sequence	"" []	SO	43767	SO:0001660	\N	core_promoter_element	SO:0001660
0	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	\N	RNA_polymerase_II_TATA_box	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	43768	SO:0001661	\N	RNA_polymerase_II_TATA_box	SO:0001661
0	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	\N	RNA_polymerase_III_TATA_box	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	43769	SO:0001662	\N	RNA_polymerase_III_TATA_box	SO:0001662
0	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	\N	BREd_motif	\N	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	43770	SO:0001663	\N	BREd_motif	SO:0001663
0	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	\N	DCE	\N	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	43771	SO:0001664	\N	DCE	SO:0001664
0	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	\N	DCE_SI	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	43772	SO:0001665	\N	DCE_SI	SO:0001665
0	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	\N	DCE_SII	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	43773	SO:0001666	\N	DCE_SII	SO:0001666
0	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	\N	DCE_SIII	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	43774	SO:0001667	\N	DCE_SIII	SO:0001667
0	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	\N	proximal_promoter_element	\N	\N	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	43775	SO:0001668	\N	proximal_promoter_element	SO:0001668
0	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	43776	SO:0001669	\N	RNApol_II_core_promoter	SO:0001669
0	"" []	\N	distal_promoter_element	\N	\N	sequence	"" []	SO	43777	SO:0001670	\N	distal_promoter_element	SO:0001670
0	"" []	\N	bacterial_RNApol_promoter_sigma_70	\N	\N	sequence	"" []	SO	43778	SO:0001671	\N	bacterial_RNApol_promoter_sigma_70	SO:0001671
0	"" []	\N	bacterial_RNApol_promoter_sigma54	\N	\N	sequence	"" []	SO	43779	SO:0001672	\N	bacterial_RNApol_promoter_sigma54	SO:0001672
0	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	\N	minus_12_signal	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	43780	SO:0001673	\N	minus_12_signal	SO:0001673
0	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	\N	minus_24_signal	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	43781	SO:0001674	\N	minus_24_signal	SO:0001674
0	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	\N	A_box_type_1	\N	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	43782	SO:0001675	\N	A_box_type_1	SO:0001675
0	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	\N	A_box_type_2	\N	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	43783	SO:0001676	\N	A_box_type_2	SO:0001676
0	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	\N	intermediate_element	\N	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	43784	SO:0001677	\N	intermediate_element	SO:0001677
0	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	\N	regulatory_promoter_element	\N	\N	sequence	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	SO	43785	SO:0001678	\N	regulatory_promoter_element	SO:0001678
0	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	\N	sequence	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SO	43786	SO:0001679	\N	transcription_regulatory_region	SO:0001679
0	"A regulatory region that is involved in the control of the process of translation." [SO:ke]	\N	translation_regulatory_region	\N	\N	sequence	"A regulatory region that is involved in the control of the process of translation." [SO:ke]	SO	43787	SO:0001680	\N	translation_regulatory_region	SO:0001680
0	"A regulatory region that is involved in the control of the process of recombination." [SO:ke]	\N	recombination_regulatory_region	\N	\N	sequence	"A regulatory region that is involved in the control of the process of recombination." [SO:ke]	SO	43788	SO:0001681	\N	recombination_regulatory_region	SO:0001681
0	"A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]	\N	replication_regulatory_region	\N	\N	sequence	"A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]	SO	43789	SO:0001682	\N	replication_regulatory_region	SO:0001682
0	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	SOFA	sequence_motif	SOFA	\N	sequence	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	SO	43790	SO:0001683	\N	sequence_motif	SO:0001683
0	"An attribute of an experimentally derived feature." [SO:ke]	\N	experimental_feature_attribute	\N	\N	sequence	"An attribute of an experimentally derived feature." [SO:ke]	SO	43791	SO:0001684	\N	experimental_feature_attribute	SO:0001684
0	"The score of an experimentally derived feature such as a p-value." [SO:ke]	\N	score	\N	\N	sequence	"The score of an experimentally derived feature such as a p-value." [SO:ke]	SO	43792	SO:0001685	\N	score	SO:0001685
0	"An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]	\N	quality_value	\N	\N	sequence	"An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]	SO	43793	SO:0001686	\N	quality_value	SO:0001686
0	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	SO	43794	SO:0001687	\N	restriction_enzyme_recognition_site	SO:0001687
0	"The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]	\N	restriction_enzyme_cleavage_junction	\N	\N	sequence	"The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]	SO	43795	SO:0001688	\N	restriction_enzyme_cleavage_junction	SO:0001688
0	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	\N	five_prime_restriction_enzyme_junction	\N	\N	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	43796	SO:0001689	\N	five_prime_restriction_enzyme_junction	SO:0001689
0	"" []	\N	three_prime_restriction_enzyme_junction	\N	\N	sequence	"" []	SO	43797	SO:0001690	\N	three_prime_restriction_enzyme_junction	SO:0001690
0	"" []	\N	blunt_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"" []	SO	43798	SO:0001691	\N	blunt_end_restriction_enzyme_cleavage_site	SO:0001691
0	"" []	\N	sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"" []	SO	43799	SO:0001692	\N	sticky_end_restriction_enzyme_cleavage_site	SO:0001692
0	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	\N	blunt_end_restriction_enzyme_cleavage_junction	\N	\N	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	43800	SO:0001693	\N	blunt_end_restriction_enzyme_cleavage_junction	SO:0001693
0	"A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]	\N	single_strand_restriction_enzyme_cleavage_site	\N	\N	sequence	"A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]	SO	43801	SO:0001694	\N	single_strand_restriction_enzyme_cleavage_site	SO:0001694
0	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	\N	restriction_enzyme_single_strand_overhang	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	SO	43802	SO:0001695	\N	restriction_enzyme_single_strand_overhang	SO:0001695
0	"A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]	\N	experimentally_defined_binding_region	\N	\N	sequence	"A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]	SO	43803	SO:0001696	\N	experimentally_defined_binding_region	SO:0001696
0	"A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]	\N	ChIP_seq_region	\N	\N	sequence	"A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]	SO	43804	SO:0001697	\N	ChIP_seq_region	SO:0001697
0	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	\N	ASPE_primer	\N	\N	sequence	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	SO	43805	SO:0001698	\N	ASPE_primer	SO:0001698
0	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	\N	dCAPS_primer	\N	\N	sequence	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	SO	43806	SO:0001699	\N	dCAPS_primer	SO:0001699
0	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	43807	SO:0001700	\N	histone_modification	SO:0001700
0	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	43808	SO:0001701	\N	histone_methylation_site	SO:0001701
0	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	43809	SO:0001702	\N	histone_acetylation_site	SO:0001702
0	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K9_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	43810	SO:0001703	\N	H3K9_acetylation_site	SO:0001703
0	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K14_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	43811	SO:0001704	\N	H3K14_acetylation_site	SO:0001704
0	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K4_monomethylation_site	\N	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43812	SO:0001705	\N	H3K4_monomethylation_site	SO:0001705
0	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K4_trimethylation	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43813	SO:0001706	\N	H3K4_trimethylation	SO:0001706
0	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K9_trimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43814	SO:0001707	\N	H3K9_trimethylation_site	SO:0001707
0	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K27_monomethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43815	SO:0001708	\N	H3K27_monomethylation_site	SO:0001708
0	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K27_trimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43816	SO:0001709	\N	H3K27_trimethylation_site	SO:0001709
0	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K79_monomethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43817	SO:0001710	\N	H3K79_monomethylation_site	SO:0001710
0	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K79_dimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43818	SO:0001711	\N	H3K79_dimethylation_site	SO:0001711
0	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H3K79_trimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43819	SO:0001712	\N	H3K79_trimethylation_site	SO:0001712
0	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H4K20_monomethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43820	SO:0001713	\N	H4K20_monomethylation_site	SO:0001713
0	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	\N	H2BK5_monomethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	43821	SO:0001714	\N	H2BK5_monomethylation_site	SO:0001714
0	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	\N	ISRE	\N	\N	sequence	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	SO	43822	SO:0001715	\N	ISRE	SO:0001715
0	"A histone modification site where ubiquitin may be added." [SO:ke]	\N	histone_ubiqitination_site	\N	\N	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	43823	SO:0001716	\N	histone_ubiqitination_site	SO:0001716
0	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	\N	H2B_ubiquitination_site	\N	\N	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	43824	SO:0001717	\N	H2B_ubiquitination_site	SO:0001717
0	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	\N	H3K18_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	43825	SO:0001718	\N	H3K18_acetylation_site	SO:0001718
0	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	\N	H3K23_acylation_site	\N	\N	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	43826	SO:0001719	\N	H3K23_acylation_site	SO:0001719
0	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SOFA	epigenetically_modified_region	SOFA	\N	sequence	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SO	43827	SO:0001720	\N	epigenetically_modified_region	SO:0001720
0	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	\N	H3K27_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	43828	SO:0001721	\N	H3K27_acylation_site	SO:0001721
0	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	\N	H3K36_monomethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	43829	SO:0001722	\N	H3K36_monomethylation_site	SO:0001722
0	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	\N	H3K36_dimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	43830	SO:0001723	\N	H3K36_dimethylation_site	SO:0001723
0	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	\N	H3K36_trimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	43831	SO:0001724	\N	H3K36_trimethylation_site	SO:0001724
0	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	\N	H3K4_dimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	43832	SO:0001725	\N	H3K4_dimethylation_site	SO:0001725
0	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	\N	H3K27_dimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	43833	SO:0001726	\N	H3K27_dimethylation_site	SO:0001726
0	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	\N	H3K9_monomethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	43834	SO:0001727	\N	H3K9_monomethylation_site	SO:0001727
0	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	\N	H3K9_dimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	43835	SO:0001728	\N	H3K9_dimethylation_site	SO:0001728
0	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	\N	H4K16_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	43836	SO:0001729	\N	H4K16_acylation_site	SO:0001729
0	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	\N	H4K5_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	43837	SO:0001730	\N	H4K5_acylation_site	SO:0001730
0	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	\N	H4K8_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	43838	SO:0001731	\N	H4K8_acylation_site	SO:0001731
0	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K27_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	43839	SO:0001732	\N	H3K27_methylation_site	SO:0001732
0	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K36_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	43840	SO:0001733	\N	H3K36_methylation_site	SO:0001733
0	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	\N	H3K4_methylation_site	\N	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	43841	SO:0001734	\N	H3K4_methylation_site	SO:0001734
0	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K79_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	43842	SO:0001735	\N	H3K79_methylation_site	SO:0001735
0	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K9_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	43843	SO:0001736	\N	H3K9_methylation_site	SO:0001736
0	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	\N	histone_acylation_region	\N	\N	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	43844	SO:0001737	\N	histone_acylation_region	SO:0001737
0	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	\N	H4K_acylation_region	\N	\N	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	43845	SO:0001738	\N	H4K_acylation_region	SO:0001738
0	"A gene with a start codon other than AUG." [SO:xp]	\N	gene_with_non_canonical_start_codon	\N	\N	sequence	"A gene with a start codon other than AUG." [SO:xp]	SO	43846	SO:0001739	\N	gene_with_non_canonical_start_codon	SO:0001739
0	"A gene with a translational start codon of CUG." [SO:mc]	\N	gene_with_start_codon_CUG	\N	\N	sequence	"A gene with a translational start codon of CUG." [SO:mc]	SO	43847	SO:0001740	\N	gene_with_start_codon_CUG	SO:0001740
0	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	\N	pseudogenic_gene_segment	\N	\N	sequence	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	SO	43848	SO:0001741	\N	pseudogenic_gene_segment	SO:0001741
0	"A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]	DBVAR	copy_number_gain	DBVAR	\N	sequence	"A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]	SO	43849	SO:0001742	\N	copy_number_gain	SO:0001742
0	"A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]	DBVAR	copy_number_loss	DBVAR	\N	sequence	"A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]	SO	43850	SO:0001743	\N	copy_number_loss	SO:0001743
0	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]	DBVAR	UPD	DBVAR	\N	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]	SO	43851	SO:0001744	\N	UPD	SO:0001744
0	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm]	\N	maternal_uniparental_disomy	\N	\N	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm]	SO	43852	SO:0001745	\N	maternal_uniparental_disomy	SO:0001745
0	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm]	\N	paternal_uniparental_disomy	\N	\N	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm]	SO	43853	SO:0001746	\N	paternal_uniparental_disomy	SO:0001746
0	"A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb]	\N	open_chromatin_region	\N	\N	sequence	"A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb]	SO	43854	SO:0001747	\N	open_chromatin_region	SO:0001747
0	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL3_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43855	SO:0001748	\N	SL3_acceptor_site	SO:0001748
0	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL4_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43856	SO:0001749	\N	SL4_acceptor_site	SO:0001749
0	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL5_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43857	SO:0001750	\N	SL5_acceptor_site	SO:0001750
0	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL6_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43858	SO:0001751	\N	SL6_acceptor_site	SO:0001751
0	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL7_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43859	SO:0001752	\N	SL7_acceptor_site	SO:0001752
0	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL8_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43860	SO:0001753	\N	SL8_acceptor_site	SO:0001753
0	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL9_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43861	SO:0001754	\N	SL9_acceptor_site	SO:0001754
0	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL10_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43862	SO:0001755	\N	SL10_acceptor_site	SO:0001755
0	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL11_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43863	SO:0001756	\N	SL11_acceptor_site	SO:0001756
0	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL12_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	43864	SO:0001757	\N	SL12_acceptor_site	SO:0001757
0	"A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]	\N	duplicated_pseudogene	\N	\N	sequence	"A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]	SO	43865	SO:0001758	\N	duplicated_pseudogene	SO:0001758
0	"A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]	\N	unitary_pseudogene	\N	\N	sequence	"A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]	SO	43866	SO:0001759	\N	unitary_pseudogene	SO:0001759
0	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	\N	non_processed_pseudogene	\N	\N	sequence	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	SO	43867	SO:0001760	\N	non_processed_pseudogene	SO:0001760
0	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	SO	43868	SO:0001761	\N	variant_quality	SO:0001761
0	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	\N	variant_origin	\N	\N	sequence	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	SO	43869	SO:0001762	\N	variant_origin	SO:0001762
0	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	\N	variant_frequency	\N	\N	sequence	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	SO	43870	SO:0001763	\N	variant_frequency	SO:0001763
0	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]	\N	unique_variant	\N	\N	sequence	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]	SO	43871	SO:0001764	\N	unique_variant	SO:0001764
0	"" []	\N	rare_variant	\N	\N	sequence	"" []	SO	43872	SO:0001765	\N	rare_variant	SO:0001765
0	"" []	\N	polymorphic_variant	\N	\N	sequence	"" []	SO	43873	SO:0001766	\N	polymorphic_variant	SO:0001766
0	"" []	\N	common_variant	\N	\N	sequence	"" []	SO	43874	SO:0001767	\N	common_variant	SO:0001767
0	"" []	\N	fixed_variant	\N	\N	sequence	"" []	SO	43875	SO:0001768	\N	fixed_variant	SO:0001768
0	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	\N	variant_phenotype	\N	\N	sequence	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	SO	43876	SO:0001769	\N	variant_phenotype	SO:0001769
0	"" []	\N	benign_variant	\N	\N	sequence	"" []	SO	43877	SO:0001770	\N	benign_variant	SO:0001770
0	"" []	\N	disease_associated_variant	\N	\N	sequence	"" []	SO	43878	SO:0001771	\N	disease_associated_variant	SO:0001771
0	"" []	\N	disease_causing_variant	\N	\N	sequence	"" []	SO	43879	SO:0001772	\N	disease_causing_variant	SO:0001772
0	"" []	\N	lethal_variant	\N	\N	sequence	"" []	SO	43880	SO:0001773	\N	lethal_variant	SO:0001773
0	"" []	\N	quantitative_variant	\N	\N	sequence	"" []	SO	43881	SO:0001774	\N	quantitative_variant	SO:0001774
0	"" []	\N	maternal_variant	\N	\N	sequence	"" []	SO	43882	SO:0001775	\N	maternal_variant	SO:0001775
0	"" []	\N	paternal_variant	\N	\N	sequence	"" []	SO	43883	SO:0001776	\N	paternal_variant	SO:0001776
0	"" []	\N	somatic_variant	\N	\N	sequence	"" []	SO	43884	SO:0001777	\N	somatic_variant	SO:0001777
0	"" []	\N	germline_variant	\N	\N	sequence	"" []	SO	43885	SO:0001778	\N	germline_variant	SO:0001778
0	"" []	\N	pedigree_specific_variant	\N	\N	sequence	"" []	SO	43886	SO:0001779	\N	pedigree_specific_variant	SO:0001779
0	"" []	\N	population_specific_variant	\N	\N	sequence	"" []	SO	43887	SO:0001780	\N	population_specific_variant	SO:0001780
0	"" []	\N	de_novo_variant	\N	\N	sequence	"" []	SO	43888	SO:0001781	\N	de_novo_variant	SO:0001781
0	"A sequence variant located within a transcription factor binding site." [EBI:fc]	\N	TF_binding_site_variant	\N	\N	sequence	"A sequence variant located within a transcription factor binding site." [EBI:fc]	SO	43889	SO:0001782	\N	TF_binding_site_variant	SO:0001782
0	"A structural sequence alteration or rearrangement encompassing one or more genome fragments." [NCBI:th, SO:ke]	DBVAR	complex_structural_alteration	DBVAR	\N	sequence	"A structural sequence alteration or rearrangement encompassing one or more genome fragments." [NCBI:th, SO:ke]	SO	43890	SO:0001784	\N	complex_structural_alteration	SO:0001784
0	"" []	DBVAR	structural_alteration	DBVAR	\N	sequence	"" []	SO	43891	SO:0001785	\N	structural_alteration	SO:0001785
0	"A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke]	DBVAR	loss_of_heterozygosity	DBVAR	\N	sequence	"A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke]	SO	43892	SO:0001786	\N	loss_of_heterozygosity	SO:0001786
0	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	\N	splice_donor_5th_base_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	43893	SO:0001787	\N	splice_donor_5th_base_variant	SO:0001787
0	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	\N	U_box	\N	\N	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	43894	SO:0001788	\N	U_box	SO:0001788
0	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	\N	mating_type_region	\N	\N	sequence	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	SO	43895	SO:0001789	\N	mating_type_region	SO:0001789
0	"An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]	SOFA	paired_end_fragment	SOFA	\N	sequence	"An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]	SO	43896	SO:0001790	\N	paired_end_fragment	SO:0001790
0	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant that changes exon sequence." [SO:ke]	SO	43897	SO:0001791	\N	exon_variant	SO:0001791
0	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	\N	non_coding_transcript_exon_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	43898	SO:0001792	\N	non_coding_transcript_exon_variant	SO:0001792
0	"A read from an end of the clone sequence." [SO:ke]	\N	clone_end	\N	\N	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	43899	SO:0001793	\N	clone_end	SO:0001793
0	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	\N	point_centromere	\N	\N	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	43900	SO:0001794	\N	point_centromere	SO:0001794
0	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	\N	regional_centromere	\N	\N	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	43901	SO:0001795	\N	regional_centromere	SO:0001795
0	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	\N	regional_centromere_central_core	\N	\N	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	43902	SO:0001796	\N	regional_centromere_central_core	SO:0001796
0	"A repeat region found within the modular centromere." [SO:ke]	\N	centromeric_repeat	\N	\N	sequence	"A repeat region found within the modular centromere." [SO:ke]	SO	43903	SO:0001797	\N	centromeric_repeat	SO:0001797
0	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	\N	regional_centromere_inner_repeat_region	\N	\N	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	43904	SO:0001798	\N	regional_centromere_inner_repeat_region	SO:0001798
0	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	\N	regional_centromere_outer_repeat_region	\N	\N	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	43905	SO:0001799	\N	regional_centromere_outer_repeat_region	SO:0001799
0	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	\N	tasiRNA	\N	\N	sequence	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	SO	43906	SO:0001800	\N	tasiRNA	SO:0001800
0	"A primary transcript encoding a tasiRNA." [PMID:16145017]	\N	tasiRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a tasiRNA." [PMID:16145017]	SO	43907	SO:0001801	\N	tasiRNA_primary_transcript	SO:0001801
0	"A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]	\N	increased_polyadenylation_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]	SO	43908	SO:0001802	\N	increased_polyadenylation_variant	SO:0001802
0	"A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]	\N	decreased_polyadenylation_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]	SO	43909	SO:0001803	\N	decreased_polyadenylation_variant	SO:0001803
0	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	\N	DDB_box	\N	\N	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	43910	SO:0001804	\N	DDB_box	SO:0001804
0	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	\N	destruction_box	\N	\N	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	43911	SO:0001805	\N	destruction_box	SO:0001805
0	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	\N	ER_retention_signal	\N	\N	sequence	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	SO	43912	SO:0001806	\N	ER_retention_signal	SO:0001806
0	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	\N	KEN_box	\N	\N	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	43913	SO:0001807	\N	KEN_box	SO:0001807
0	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	\N	mitochondrial_targeting_signal	\N	\N	sequence	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	SO	43914	SO:0001808	\N	mitochondrial_targeting_signal	SO:0001808
0	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	\N	signal_anchor	\N	\N	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	43915	SO:0001809	\N	signal_anchor	SO:0001809
0	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	\N	PIP_box	\N	\N	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	43916	SO:0001810	\N	PIP_box	SO:0001810
0	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	\N	phosphorylation_site	\N	\N	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	43917	SO:0001811	\N	phosphorylation_site	SO:0001811
0	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	\N	transmembrane_helix	\N	\N	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	43918	SO:0001812	\N	transmembrane_helix	SO:0001812
0	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	\N	vacuolar_sorting_signal	\N	\N	sequence	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	SO	43919	SO:0001813	\N	vacuolar_sorting_signal	SO:0001813
0	"" []	\N	coding_variant_quality	\N	\N	sequence	"" []	SO	43920	SO:0001814	\N	coding_variant_quality	SO:0001814
0	"" []	\N	synonymous	\N	\N	sequence	"" []	SO	43921	SO:0001815	\N	synonymous	SO:0001815
0	"" []	\N	non_synonymous	\N	\N	sequence	"" []	SO	43922	SO:0001816	\N	non_synonymous	SO:0001816
0	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]	\N	inframe	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]	SO	43923	SO:0001817	\N	inframe	SO:0001817
0	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	43924	SO:0001818	\N	protein_altering_variant	SO:0001818
0	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	\N	synonymous_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	43925	SO:0001819	\N	synonymous_variant	SO:0001819
0	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	\N	inframe_indel	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	43926	SO:0001820	\N	inframe_indel	SO:0001820
0	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	\N	inframe_insertion	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	43927	SO:0001821	\N	inframe_insertion	SO:0001821
0	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	\N	inframe_deletion	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	43928	SO:0001822	\N	inframe_deletion	SO:0001822
0	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	\N	conservative_inframe_insertion	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	43929	SO:0001823	\N	conservative_inframe_insertion	SO:0001823
0	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	\N	disruptive_inframe_insertion	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	43930	SO:0001824	\N	disruptive_inframe_insertion	SO:0001824
0	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	\N	conservative_inframe_deletion	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	43931	SO:0001825	\N	conservative_inframe_deletion	SO:0001825
0	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	\N	disruptive_inframe_deletion	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	43932	SO:0001826	\N	disruptive_inframe_deletion	SO:0001826
0	"A sequencer read of an mRNA substrate." [SO:ke]	\N	mRNA_read	\N	\N	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	43933	SO:0001827	\N	mRNA_read	SO:0001827
0	"A sequencer read of a genomic DNA substrate." [SO:ke]	\N	genomic_DNA_read	\N	\N	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	43934	SO:0001828	\N	genomic_DNA_read	SO:0001828
0	"A contig composed of mRNA_reads." [SO:ke]	\N	mRNA_contig	\N	\N	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	43935	SO:0001829	\N	mRNA_contig	SO:0001829
0	"A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]	\N	AFLP_fragment	\N	\N	sequence	"A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]	SO	43936	SO:0001830	\N	AFLP_fragment	SO:0001830
0	"A match to a protein HMM such as pfam." [SO:ke]	\N	protein_hmm_match	\N	\N	sequence	"A match to a protein HMM such as pfam." [SO:ke]	SO	43937	SO:0001831	\N	protein_hmm_match	SO:0001831
0	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	\N	immunoglobulin_region	\N	\N	sequence	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	SO	43938	SO:0001832	\N	immunoglobulin_region	SO:0001832
0	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	\N	V_region	\N	\N	sequence	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	43939	SO:0001833	\N	V_region	SO:0001833
0	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	\N	C_region	\N	\N	sequence	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	43940	SO:0001834	\N	C_region	SO:0001834
0	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	\N	N_region	\N	\N	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	43941	SO:0001835	\N	N_region	SO:0001835
0	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	\N	S_region	\N	\N	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	43942	SO:0001836	\N	S_region	SO:0001836
0	"A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]	\N	mobile_element_insertion	\N	\N	sequence	"A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]	SO	43943	SO:0001837	\N	mobile_element_insertion	SO:0001837
0	"An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]	\N	novel_sequence_insertion	\N	\N	sequence	"An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]	SO	43944	SO:0001838	\N	novel_sequence_insertion	SO:0001838
0	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	\N	CSL_response_element	\N	\N	sequence	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	SO	43945	SO:0001839	\N	CSL_response_element	SO:0001839
0	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	\N	GATA_box	\N	\N	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	43946	SO:0001840	\N	GATA_box	SO:0001840
0	"Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]	\N	polymorphic_pseudogene	\N	\N	sequence	"Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]	SO	43947	SO:0001841	\N	polymorphic_pseudogene	SO:0001841
0	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	\N	AP_1_binding_site	\N	\N	sequence	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	SO	43948	SO:0001842	\N	AP_1_binding_site	SO:0001842
0	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	\N	CRE	\N	\N	sequence	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	SO	43949	SO:0001843	\N	CRE	SO:0001843
0	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	\N	CuRE	\N	\N	sequence	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	SO	43950	SO:0001844	\N	CuRE	SO:0001844
0	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	\N	DRE	\N	\N	sequence	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	SO	43951	SO:0001845	\N	DRE	SO:0001845
0	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	\N	FLEX_element	\N	\N	sequence	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	SO	43952	SO:0001846	\N	FLEX_element	SO:0001846
0	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	\N	forkhead_motif	\N	\N	sequence	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	SO	43953	SO:0001847	\N	forkhead_motif	SO:0001847
0	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	\N	homol_D_box	\N	\N	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	43954	SO:0001848	\N	homol_D_box	SO:0001848
0	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	\N	homol_E_box	\N	\N	sequence	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	SO	43955	SO:0001849	\N	homol_E_box	SO:0001849
0	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	\N	HSE	\N	\N	sequence	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	SO	43956	SO:0001850	\N	HSE	SO:0001850
0	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	\N	iron_repressed_GATA_element	\N	\N	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	43957	SO:0001851	\N	iron_repressed_GATA_element	SO:0001851
0	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	\N	mating_type_M_box	\N	\N	sequence	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	SO	43958	SO:0001852	\N	mating_type_M_box	SO:0001852
0	"A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]	\N	androgen_response_element	\N	\N	sequence	"A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]	SO	43959	SO:0001853	\N	androgen_response_element	SO:0001853
0	"A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]	\N	smFISH_probe	\N	\N	sequence	"A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]	SO	43960	SO:0001854	\N	smFISH_probe	SO:0001854
0	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	\N	MCB	\N	\N	sequence	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	SO	43961	SO:0001855	\N	MCB	SO:0001855
0	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	\N	CCAAT_motif	\N	\N	sequence	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	SO	43962	SO:0001856	\N	CCAAT_motif	SO:0001856
0	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	\N	Ace2_UAS	\N	\N	sequence	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	SO	43963	SO:0001857	\N	Ace2_UAS	SO:0001857
0	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	\N	TR_box	\N	\N	sequence	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	SO	43964	SO:0001858	\N	TR_box	SO:0001858
0	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	\N	STREP_motif	\N	\N	sequence	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	SO	43965	SO:0001859	\N	STREP_motif	SO:0001859
0	"A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]	\N	rDNA_intergenic_spacer_element	\N	\N	sequence	"A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]	SO	43966	SO:0001860	\N	rDNA_intergenic_spacer_element	SO:0001860
0	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	\N	sterol_regulatory_element	\N	\N	sequence	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	SO	43967	SO:0001861	\N	sterol_regulatory_element	SO:0001861
0	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	\N	GT_dinucleotide_repeat	\N	\N	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	43968	SO:0001862	\N	GT_dinucleotide_repeat	SO:0001862
0	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	\N	GTT_trinucleotide_repeat	\N	\N	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	43969	SO:0001863	\N	GTT_trinucleotide_repeat	SO:0001863
0	"A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]	\N	Sap1_recognition_motif	\N	\N	sequence	"A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]	SO	43970	SO:0001864	\N	Sap1_recognition_motif	SO:0001864
0	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	\N	CDRE_motif	\N	\N	sequence	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	SO	43971	SO:0001865	\N	CDRE_motif	SO:0001865
0	"A contig of BAC reads." [GMOD:ea]	\N	BAC_read_contig	\N	\N	sequence	"A contig of BAC reads." [GMOD:ea]	SO	43972	SO:0001866	\N	BAC_read_contig	SO:0001866
0	"A gene suspected of being involved in the expression of a trait." [GMOD:ea]	\N	candidate_gene	\N	\N	sequence	"A gene suspected of being involved in the expression of a trait." [GMOD:ea]	SO	43973	SO:0001867	\N	candidate_gene	SO:0001867
0	"A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]	\N	positional_candidate_gene	\N	\N	sequence	"A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]	SO	43974	SO:0001868	\N	positional_candidate_gene	SO:0001868
0	"A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]	\N	functional_candidate_gene	\N	\N	sequence	"A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]	SO	43975	SO:0001869	\N	functional_candidate_gene	SO:0001869
0	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	\N	enhancerRNA	\N	\N	sequence	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	SO	43976	SO:0001870	\N	enhancerRNA	SO:0001870
0	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	\N	PCB	\N	\N	sequence	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	SO	43977	SO:0001871	\N	PCB	SO:0001871
0	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	\N	rearrangement_breakpoint	\N	\N	sequence	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	SO	43978	SO:0001872	\N	rearrangement_breakpoint	SO:0001872
0	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	\N	interchromosomal_breakpoint	\N	\N	sequence	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	SO	43979	SO:0001873	\N	interchromosomal_breakpoint	SO:0001873
0	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	\N	intrachromosomal_breakpoint	\N	\N	sequence	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	SO	43980	SO:0001874	\N	intrachromosomal_breakpoint	SO:0001874
0	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	\N	unassigned_supercontig	\N	\N	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	43981	SO:0001875	\N	unassigned_supercontig	SO:0001875
0	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	\N	sequence	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SO	43982	SO:0001876	\N	partial_genomic_sequence_assembly	SO:0001876
0	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	\N	lnc_RNA	\N	\N	sequence	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	SO	43983	SO:0001877	\N	lnc_RNA	SO:0001877
0	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	SO	43984	SO:0001878	\N	feature_variant	SO:0001878
0	"A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_ablation	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]	SO	43985	SO:0001879	\N	feature_ablation	SO:0001879
0	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_amplification	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]	SO	43986	SO:0001880	\N	feature_amplification	SO:0001880
0	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_translocation	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]	SO	43987	SO:0001881	\N	feature_translocation	SO:0001881
0	"A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]	\N	feature_fusion	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]	SO	43988	SO:0001882	\N	feature_fusion	SO:0001882
0	"A feature translocation where the region contains a transcript." [SO:ke]	\N	transcript_translocation	\N	\N	sequence	"A feature translocation where the region contains a transcript." [SO:ke]	SO	43989	SO:0001883	\N	transcript_translocation	SO:0001883
0	"A feature translocation where the region contains a regulatory region." [SO:ke]	\N	regulatory_region_translocation	\N	\N	sequence	"A feature translocation where the region contains a regulatory region." [SO:ke]	SO	43990	SO:0001884	\N	regulatory_region_translocation	SO:0001884
0	"A feature translocation where the region contains a transcription factor binding site." [SO:ke]	\N	TFBS_translocation	\N	\N	sequence	"A feature translocation where the region contains a transcription factor binding site." [SO:ke]	SO	43991	SO:0001885	\N	TFBS_translocation	SO:0001885
0	"A feature fusion where the deletion brings together transcript regions." [SO:ke]	\N	transcript_fusion	\N	\N	sequence	"A feature fusion where the deletion brings together transcript regions." [SO:ke]	SO	43992	SO:0001886	\N	transcript_fusion	SO:0001886
0	"A feature fusion where the deletion brings together regulatory regions." [SO:ke]	\N	regulatory_region_fusion	\N	\N	sequence	"A feature fusion where the deletion brings together regulatory regions." [SO:ke]	SO	43993	SO:0001887	\N	regulatory_region_fusion	SO:0001887
0	"A fusion where the deletion brings together transcription factor binding sites." [SO:ke]	\N	TFBS_fusion	\N	\N	sequence	"A fusion where the deletion brings together transcription factor binding sites." [SO:ke]	SO	43994	SO:0001888	\N	TFBS_fusion	SO:0001888
0	"A feature amplification of a region containing a transcript." [SO:ke]	\N	transcript_amplification	\N	\N	sequence	"A feature amplification of a region containing a transcript." [SO:ke]	SO	43995	SO:0001889	\N	transcript_amplification	SO:0001889
0	"A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]	\N	transcript_regulatory_region_fusion	\N	\N	sequence	"A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]	SO	43996	SO:0001890	\N	transcript_regulatory_region_fusion	SO:0001890
0	"A feature amplification of a region containing a regulatory region." [SO:ke]	\N	regulatory_region_amplification	\N	\N	sequence	"A feature amplification of a region containing a regulatory region." [SO:ke]	SO	43997	SO:0001891	\N	regulatory_region_amplification	SO:0001891
0	"A feature amplification of a region containing a transcription factor binding site." [SO:ke]	\N	TFBS_amplification	\N	\N	sequence	"A feature amplification of a region containing a transcription factor binding site." [SO:ke]	SO	43998	SO:0001892	\N	TFBS_amplification	SO:0001892
0	"A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]	\N	transcript_ablation	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]	SO	43999	SO:0001893	\N	transcript_ablation	SO:0001893
0	"A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]	\N	regulatory_region_ablation	\N	\N	sequence	"A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]	SO	44000	SO:0001894	\N	regulatory_region_ablation	SO:0001894
0	"A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]	\N	TFBS_ablation	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]	SO	44001	SO:0001895	\N	TFBS_ablation	SO:0001895
0	"A CDS that is part of a transposable element." [SO:ke]	\N	transposable_element_CDS	\N	\N	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	44002	SO:0001896	\N	transposable_element_CDS	SO:0001896
0	"A pseudogene contained within a transposable element." [SO:ke]	\N	transposable_element_pseudogene	\N	\N	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	44003	SO:0001897	\N	transposable_element_pseudogene	SO:0001897
0	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	\N	dg_repeat	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	44004	SO:0001898	\N	dg_repeat	SO:0001898
0	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	\N	dh_repeat	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	44005	SO:0001899	\N	dh_repeat	SO:0001899
0	"A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]	\N	M26_binding_site	\N	\N	sequence	"A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]	SO	44006	SO:0001900	\N	M26_binding_site	SO:0001900
0	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	\N	AACCCT_box	\N	\N	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	44007	SO:0001901	\N	AACCCT_box	SO:0001901
0	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	\N	splice_region	\N	\N	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	44008	SO:0001902	\N	splice_region	SO:0001902
0	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	\N	intronic_lncRNA	\N	\N	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	44009	SO:0001903	\N	intronic_lncRNA	SO:0001903
0	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	\N	antisense_lncRNA	\N	\N	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	44010	SO:0001904	\N	antisense_lncRNA	SO:0001904
0	"A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]	\N	regional_centromere_outer_repeat_transcript	\N	\N	sequence	"A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]	SO	44011	SO:0001905	\N	regional_centromere_outer_repeat_transcript	SO:0001905
0	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_truncation	\N	\N	sequence	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	SO	44012	SO:0001906	\N	feature_truncation	SO:0001906
0	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_elongation	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	SO	44013	SO:0001907	\N	feature_elongation	SO:0001907
0	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	\N	internal_feature_elongation	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	SO	44014	SO:0001908	\N	internal_feature_elongation	SO:0001908
0	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	\N	frameshift_elongation	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	44015	SO:0001909	\N	frameshift_elongation	SO:0001909
0	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	\N	frameshift_truncation	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	44016	SO:0001910	\N	frameshift_truncation	SO:0001910
0	"A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]	\N	copy_number_increase	\N	\N	sequence	"A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]	SO	44017	SO:0001911	\N	copy_number_increase	SO:0001911
0	"A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]	\N	copy_number_decrease	\N	\N	sequence	"A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]	SO	44018	SO:0001912	\N	copy_number_decrease	SO:0001912
0	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	\N	bacterial_RNApol_promoter_sigma_ecf	\N	\N	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	44019	SO:0001913	\N	bacterial_RNApol_promoter_sigma_ecf	SO:0001913
0	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]	\N	rDNA_replication_fork_barrier	\N	\N	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]	SO	44020	SO:0001914	\N	rDNA_replication_fork_barrier	SO:0001914
0	"A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]	\N	transcription_start_cluster	\N	\N	sequence	"A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]	SO	44021	SO:0001915	\N	transcription_start_cluster	SO:0001915
0	"A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]	\N	CAGE_tag	\N	\N	sequence	"A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]	SO	44022	SO:0001916	\N	CAGE_tag	SO:0001916
0	"A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]	\N	CAGE_cluster	\N	\N	sequence	"A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]	SO	44023	SO:0001917	\N	CAGE_cluster	SO:0001917
0	"A cytosine methylated at the 5 carbon." [SO:rtapella]	\N	5_methylcytosine	\N	\N	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	44024	SO:0001918	\N	5_methylcytosine	SO:0001918
0	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	\N	4_methylcytosine	\N	\N	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	44025	SO:0001919	\N	4_methylcytosine	SO:0001919
0	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	\N	N6_methyladenine	\N	\N	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	44026	SO:0001920	\N	N6_methyladenine	SO:0001920
0	"A contig of mitochondria derived sequences." [GMOD:ea]	\N	mitochondrial_contig	\N	\N	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	44027	SO:0001921	\N	mitochondrial_contig	SO:0001921
0	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	\N	mitochondrial_supercontig	\N	\N	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	44028	SO:0001922	\N	mitochondrial_supercontig	SO:0001922
0	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	\N	TERRA	\N	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	44029	SO:0001923	\N	TERRA	SO:0001923
0	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	\N	ARRET	\N	\N	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	44030	SO:0001924	\N	ARRET	SO:0001924
0	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	\N	ARIA	\N	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	44031	SO:0001925	\N	ARIA	SO:0001925
0	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	\N	anti_ARRET	\N	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	44032	SO:0001926	\N	anti_ARRET	SO:0001926
0	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	\N	telomeric_transcript	\N	\N	sequence	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	SO	44033	SO:0001927	\N	telomeric_transcript	SO:0001927
0	"A duplication of the distal region of a chromosome." [SO:bm]	\N	distal_duplication	\N	\N	sequence	"A duplication of the distal region of a chromosome." [SO:bm]	SO	44034	SO:0001928	\N	distal_duplication	SO:0001928
0	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	\N	mitochondrial_DNA_read	\N	\N	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	44035	SO:0001929	\N	mitochondrial_DNA_read	SO:0001929
0	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	\N	chloroplast_DNA_read	\N	\N	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	44036	SO:0001930	\N	chloroplast_DNA_read	SO:0001930
0	"Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]	\N	consensus_gDNA	\N	\N	sequence	"Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]	SO	44037	SO:0001931	\N	consensus_gDNA	SO:0001931
0	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	\N	restriction_enzyme_five_prime_single_strand_overhang	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	44038	SO:0001932	\N	restriction_enzyme_five_prime_single_strand_overhang	SO:0001932
0	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	\N	restriction_enzyme_three_prime_single_strand_overhang	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	44039	SO:0001933	\N	restriction_enzyme_three_prime_single_strand_overhang	SO:0001933
0	"A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]	\N	monomeric_repeat	\N	\N	sequence	"A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]	SO	44040	SO:0001934	\N	monomeric_repeat	SO:0001934
0	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	\N	H3K20_trimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	44041	SO:0001935	\N	H3K20_trimethylation_site	SO:0001935
0	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	\N	H3K36_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	44042	SO:0001936	\N	H3K36_acetylation_site	SO:0001936
0	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	\N	H2BK12_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	44043	SO:0001937	\N	H2BK12_acetylation_site	SO:0001937
0	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	\N	H2AK5_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	44044	SO:0001938	\N	H2AK5_acetylation_site	SO:0001938
0	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	\N	H4K12_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	44045	SO:0001939	\N	H4K12_acetylation_site	SO:0001939
0	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	\N	H2BK120_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	44046	SO:0001940	\N	H2BK120_acetylation_site	SO:0001940
0	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	\N	H4K91_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	44047	SO:0001941	\N	H4K91_acetylation_site	SO:0001941
0	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	\N	H2BK20_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	44048	SO:0001942	\N	H2BK20_acetylation_site	SO:0001942
0	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	\N	H3K4ac_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	44049	SO:0001943	\N	H3K4ac_acetylation_site	SO:0001943
0	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	\N	H2AK9_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	44050	SO:0001944	\N	H2AK9_acetylation_site	SO:0001944
0	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	\N	H3K56_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	44051	SO:0001945	\N	H3K56_acetylation_site	SO:0001945
0	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	\N	H2BK15_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	44052	SO:0001946	\N	H2BK15_acetylation_site	SO:0001946
0	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	\N	H3R2_monomethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	44053	SO:0001947	\N	H3R2_monomethylation_site	SO:0001947
0	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	\N	H3R2_dimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	44054	SO:0001948	\N	H3R2_dimethylation_site	SO:0001948
0	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	\N	H4R3_dimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	44055	SO:0001949	\N	H4R3_dimethylation_site	SO:0001949
0	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	\N	H4K4_trimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	44056	SO:0001950	\N	H4K4_trimethylation_site	SO:0001950
0	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	\N	H3K23_dimethylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	44057	SO:0001951	\N	H3K23_dimethylation_site	SO:0001951
0	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	\N	promoter_flanking_region	\N	\N	sequence	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	SO	44058	SO:0001952	\N	promoter_flanking_region	SO:0001952
0	"A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]	\N	restriction_enzyme_assembly_scar	\N	\N	sequence	"A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]	SO	44059	SO:0001953	\N	restriction_enzyme_assembly_scar	SO:0001953
0	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A region related to restriction enzyme function." [SO:ke]	SO	44060	SO:0001954	\N	restriction_enzyme_region	SO:0001954
0	"A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]	\N	protein_stability_element	\N	\N	sequence	"A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]	SO	44061	SO:0001955	\N	protein_stability_element	SO:0001955
0	"A polypeptide_region that  codes for a protease cleavage site." [SO:ke]	\N	protease_site	\N	\N	sequence	"A polypeptide_region that  codes for a protease cleavage site." [SO:ke]	SO	44062	SO:0001956	\N	protease_site	SO:0001956
0	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	\N	lariat_intron	\N	\N	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	44063	SO:0001958	\N	lariat_intron	SO:0001958
0	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	\N	TCT_motif	\N	\N	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	44064	SO:0001959	\N	TCT_motif	SO:0001959
0	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	\N	5_hydroxymethylcytosine	\N	\N	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	44065	SO:0001960	\N	5_hydroxymethylcytosine	SO:0001960
0	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	\N	5_formylcytosine	\N	\N	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	44066	SO:0001961	\N	5_formylcytosine	SO:0001961
0	"A modified adenine DNA base feature." [SO:ke]	\N	modified_adenine	\N	\N	sequence	"A modified adenine DNA base feature." [SO:ke]	SO	44067	SO:0001962	\N	modified_adenine	SO:0001962
0	"A modified cytosine DNA base feature." [SO:ke]	\N	modified_cytosine	\N	\N	sequence	"A modified cytosine DNA base feature." [SO:ke]	SO	44068	SO:0001963	\N	modified_cytosine	SO:0001963
0	"A modified guanine DNA base feature." [SO:ke]	\N	modified_guanine	\N	\N	sequence	"A modified guanine DNA base feature." [SO:ke]	SO	44069	SO:0001964	\N	modified_guanine	SO:0001964
0	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	\N	8_oxoguanine	\N	\N	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	44070	SO:0001965	\N	8_oxoguanine	SO:0001965
0	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	\N	5_carboxylcytosine	\N	\N	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	44071	SO:0001966	\N	5_carboxylcytosine	SO:0001966
0	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	\N	8_oxoadenine	\N	\N	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	44072	SO:0001967	\N	8_oxoadenine	SO:0001967
0	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A transcript variant of a protein coding gene." [SO:ke]	SO	44073	SO:0001968	\N	coding_transcript_variant	SO:0001968
0	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	\N	coding_transcript_intron_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	44074	SO:0001969	\N	coding_transcript_intron_variant	SO:0001969
0	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	\N	non_coding_transcript_intron_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	44075	SO:0001970	\N	non_coding_transcript_intron_variant	SO:0001970
0	"" []	\N	zinc_finger_binding_site	\N	\N	sequence	"" []	SO	44076	SO:0001971	\N	zinc_finger_binding_site	SO:0001971
0	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_4_acylation_site	\N	\N	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	44077	SO:0001972	\N	histone_4_acylation_site	SO:0001972
0	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	44078	SO:0001973	\N	histone_3_acetylation_site	SO:0001973
0	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	\N	CTCF_binding_site	\N	\N	sequence	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	SO	44079	SO:0001974	\N	CTCF_binding_site	SO:0001974
0	"A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]	\N	five_prime_sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]	SO	44080	SO:0001975	\N	five_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001975
0	"A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]	\N	three_prime_sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]	SO	44081	SO:0001976	\N	three_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001976
0	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	\N	ribonuclease_site	\N	\N	sequence	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	SO	44082	SO:0001977	\N	ribonuclease_site	SO:0001977
0	"A region of  sequence where developer information is encoded." [SO:ke]	\N	signature	\N	\N	sequence	"A region of  sequence where developer information is encoded." [SO:ke]	SO	44083	SO:0001978	\N	signature	SO:0001978
0	"A motif that affects the stability of RNA." [PMID:22495308, SO:ke]	\N	RNA_stability_element	\N	\N	sequence	"A motif that affects the stability of RNA." [PMID:22495308, SO:ke]	SO	44084	SO:0001979	\N	RNA_stability_element	SO:0001979
0	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	\N	G_box	\N	\N	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	44085	SO:0001980	\N	G_box	SO:0001980
0	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	\N	L_box	\N	\N	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	44086	SO:0001981	\N	L_box	SO:0001981
0	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	\N	I-box	\N	\N	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	44087	SO:0001982	\N	I-box	SO:0001982
0	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	\N	5_prime_UTR_premature_start_codon_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	44088	SO:0001983	\N	5_prime_UTR_premature_start_codon_variant	SO:0001983
0	"A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]	\N	silent_mating_type_cassette_array	\N	\N	sequence	"A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]	SO	44089	SO:0001984	\N	silent_mating_type_cassette_array	SO:0001984
0	"Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]	\N	Okazaki_fragment	\N	\N	sequence	"Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]	SO	44090	SO:0001985	\N	Okazaki_fragment	SO:0001985
0	"A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]	\N	upstream_transcript_variant	\N	\N	sequence	"A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]	SO	44091	SO:0001986	\N	upstream_transcript_variant	SO:0001986
0	"" []	\N	downstream_transcript_variant	\N	\N	sequence	"" []	SO	44092	SO:0001987	\N	downstream_transcript_variant	SO:0001987
0	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	\N	5_prime_UTR_premature_start_codon_gain_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	44093	SO:0001988	\N	5_prime_UTR_premature_start_codon_gain_variant	SO:0001988
0	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	\N	5_prime_UTR_premature_start_codon_loss_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	44094	SO:0001989	\N	5_prime_UTR_premature_start_codon_loss_variant	SO:0001989
0	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	\N	five_prime_UTR_premature_start_codon_location_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	44095	SO:0001990	\N	five_prime_UTR_premature_start_codon_location_variant	SO:0001990
0	"A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]	\N	consensus_AFLP_fragment	\N	\N	sequence	"A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]	SO	44096	SO:0001991	\N	consensus_AFLP_fragment	SO:0001991
0	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	44097	SO:0001992	\N	nonsynonymous_variant	SO:0001992
0	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	\N	extended_cis_splice_site	\N	\N	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	44098	SO:0001993	\N	extended_cis_splice_site	SO:0001993
0	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	\N	intron_base_5	\N	\N	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	44099	SO:0001994	\N	intron_base_5	SO:0001994
0	"A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]	\N	extended_intronic_splice_region_variant	\N	\N	sequence	"A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]	SO	44100	SO:0001995	\N	extended_intronic_splice_region_variant	SO:0001995
0	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	\N	extended_intronic_splice_region	\N	\N	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	44101	SO:0001996	\N	extended_intronic_splice_region	SO:0001996
0	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	\N	subtelomere	\N	\N	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	44102	SO:0001997	\N	subtelomere	SO:0001997
0	"A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]	\N	sgRNA	\N	\N	sequence	"A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]	SO	44103	SO:0001998	\N	sgRNA	SO:0001998
0	"DNA motif that is a component of a mating type region." [SO:ke]	\N	mating_type_region_motif	\N	\N	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	44104	SO:0001999	\N	mating_type_region_motif	SO:0001999
0	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	\N	W_region	\N	\N	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	44105	SO:0002000	\N	W_region	SO:0002000
0	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	\N	Y_region	\N	\N	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	44106	SO:0002001	\N	Y_region	SO:0002001
0	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	\N	Z1_region	\N	\N	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	44107	SO:0002002	\N	Z1_region	SO:0002002
0	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	\N	Z2_region	\N	\N	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	44108	SO:0002003	\N	Z2_region	SO:0002003
0	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	\N	ARS_consensus_sequence	\N	\N	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	44109	SO:0002004	\N	ARS_consensus_sequence	SO:0002004
0	"The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]	\N	DSR_motif	\N	\N	sequence	"The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]	SO	44110	SO:0002005	\N	DSR_motif	SO:0002005
0	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	\N	zinc_repressed_element	\N	\N	sequence	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	SO	44111	SO:0002006	\N	zinc_repressed_element	SO:0002006
0	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	\N	MNV	\N	\N	sequence	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	SO	44112	SO:0002007	\N	MNV	SO:0002007
0	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	\N	rare_amino_acid_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	44113	SO:0002008	\N	rare_amino_acid_variant	SO:0002008
0	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	\N	selenocysteine_loss	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	44114	SO:0002009	\N	selenocysteine_loss	SO:0002009
0	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	\N	pyrrolysine_loss	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	44115	SO:0002010	\N	pyrrolysine_loss	SO:0002010
0	"A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence." [SO:ke]	\N	intragenic_variant	\N	\N	sequence	"A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence." [SO:ke]	SO	44116	SO:0002011	\N	intragenic_variant	SO:0002011
0	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	\N	start_lost	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	44117	SO:0002012	\N	start_lost	SO:0002012
0	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	\N	5_prime_UTR_truncation	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	44118	SO:0002013	\N	5_prime_UTR_truncation	SO:0002013
0	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	\N	5_prime_UTR_elongation	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	44119	SO:0002014	\N	5_prime_UTR_elongation	SO:0002014
0	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	\N	3_prime_UTR_truncation	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	44120	SO:0002015	\N	3_prime_UTR_truncation	SO:0002015
0	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	\N	3_prime_UTR_elongation	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	44121	SO:0002016	\N	3_prime_UTR_elongation	SO:0002016
0	"A sequence variant located in a conserved intergenic region, between genes." [SO:ke]	\N	conserved_intergenic_variant	\N	\N	sequence	"A sequence variant located in a conserved intergenic region, between genes." [SO:ke]	SO	44122	SO:0002017	\N	conserved_intergenic_variant	SO:0002017
0	"A transcript variant occurring within a conserved region of an intron." [SO:ke]	\N	conserved_intron_variant	\N	\N	sequence	"A transcript variant occurring within a conserved region of an intron." [SO:ke]	SO	44123	SO:0002018	\N	conserved_intron_variant	SO:0002018
0	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	\N	start_retained_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	44124	SO:0002019	\N	start_retained_variant	SO:0002019
0	"Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]	\N	boundary_element	\N	\N	sequence	"Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]	SO	44125	SO:0002020	\N	boundary_element	SO:0002020
0	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]	\N	mating_type_region_replication_fork_barrier	\N	\N	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]	SO	44126	SO:0002021	\N	mating_type_region_replication_fork_barrier	SO:0002021
0	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	\N	priRNA	\N	\N	sequence	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	SO	44127	SO:0002022	\N	priRNA	SO:0002022
0	"A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]	\N	multiplexing_sequence_identifier	\N	\N	sequence	"A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]	SO	44128	SO:0002023	\N	multiplexing_sequence_identifier	SO:0002023
0	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	\N	W_region	\N	\N	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	44129	SO:0002024	\N	W_region	SO:0002024
0	"A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	\N	cis_acting_homologous_chromosome_pairing_region	\N	\N	sequence	"A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	SO	44130	SO:0002025	\N	cis_acting_homologous_chromosome_pairing_region	SO:0002025
0	"The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]	\N	intein_encoding_region	\N	\N	sequence	"The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]	SO	44131	SO:0002026	\N	intein_encoding_region	SO:0002026
0	"A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]	\N	uORF	\N	\N	sequence	"A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]	SO	44132	SO:0002027	\N	uORF	SO:0002027
0	"An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]	\N	sORF	\N	\N	sequence	"An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]	SO	44133	SO:0002028	\N	sORF	SO:0002028
0	"A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]	\N	tnaORF	\N	\N	sequence	"A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]	SO	44134	SO:0002029	\N	tnaORF	SO:0002029
0	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	\N	X_region	\N	\N	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	44135	SO:0002030	\N	X_region	SO:0002030
0	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	\N	shRNA	\N	\N	sequence	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	SO	44136	SO:0002031	\N	shRNA	SO:0002031
0	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	\N	sequence	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SO	44137	SO:0005836	\N	regulatory_region	SO:0005836
0	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	\N	U14_snoRNA_primary_transcript	\N	\N	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	44138	SO:0005837	\N	U14_snoRNA_primary_transcript	SO:0005837
0	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	\N	methylation_guide_snoRNA	\N	\N	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	44139	SO:0005841	\N	methylation_guide_snoRNA	SO:0005841
0	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	\N	rRNA_cleavage_RNA	\N	\N	sequence	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	SO	44140	SO:0005843	\N	rRNA_cleavage_RNA	SO:0005843
0	"An exon that is the only exon in a gene." [RSC:cb]	\N	exon_of_single_exon_gene	\N	\N	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	44141	SO:0005845	\N	exon_of_single_exon_gene	SO:0005845
0	"" []	\N	cassette_array_member	\N	\N	sequence	"" []	SO	44142	SO:0005847	\N	cassette_array_member	SO:0005847
0	"" []	\N	gene_cassette_member	\N	\N	sequence	"" []	SO	44143	SO:0005848	\N	gene_cassette_member	SO:0005848
0	"" []	\N	gene_subarray_member	\N	\N	sequence	"" []	SO	44144	SO:0005849	\N	gene_subarray_member	SO:0005849
0	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	primer_binding_site	\N	\N	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	44145	SO:0005850	\N	primer_binding_site	SO:0005850
0	"An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]	\N	gene_array	\N	\N	sequence	"An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]	SO	44146	SO:0005851	\N	gene_array	SO:0005851
0	"A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]	\N	gene_subarray	\N	\N	sequence	"A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]	SO	44147	SO:0005852	\N	gene_subarray	SO:0005852
0	"A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]	\N	gene_cassette	\N	\N	sequence	"A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]	SO	44148	SO:0005853	\N	gene_cassette	SO:0005853
0	"An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]	\N	gene_cassette_array	\N	\N	sequence	"An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]	SO	44149	SO:0005854	\N	gene_cassette_array	SO:0005854
0	"A collection of related genes." [SO:ma]	SOFA	gene_group	SOFA	\N	sequence	"A collection of related genes." [SO:ma]	SO	44150	SO:0005855	\N	gene_group	SO:0005855
0	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	\N	selenocysteine_tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	44151	SO:0005856	\N	selenocysteine_tRNA_primary_transcript	SO:0005856
0	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	\N	selenocysteinyl_tRNA	\N	\N	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	44152	SO:0005857	\N	selenocysteinyl_tRNA	SO:0005857
0	"A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]	\N	syntenic_region	\N	\N	sequence	"A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]	SO	44153	SO:0005858	\N	syntenic_region	SO:0005858
0	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	\N	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	44154	SO:0100001	\N	biochemical_region_of_peptide	SO:0100001
0	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	\N	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	44155	SO:0100002	\N	molecular_contact_region	SO:0100002
0	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	biosapiens	intrinsically_unstructured_polypeptide_region	biosapiens	\N	sequence	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	SO	44156	SO:0100003	\N	intrinsically_unstructured_polypeptide_region	SO:0100003
0	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	catmat_left_handed_three	biosapiens	\N	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	44157	SO:0100004	\N	catmat_left_handed_three	SO:0100004
0	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	catmat_left_handed_four	biosapiens	\N	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	44158	SO:0100005	\N	catmat_left_handed_four	SO:0100005
0	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	catmat_right_handed_three	biosapiens	\N	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	44159	SO:0100006	\N	catmat_right_handed_three	SO:0100006
0	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	catmat_right_handed_four	biosapiens	\N	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	44160	SO:0100007	\N	catmat_right_handed_four	SO:0100007
0	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	alpha_beta_motif	biosapiens	\N	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	44161	SO:0100008	\N	alpha_beta_motif	SO:0100008
0	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	biosapiens	lipoprotein_signal_peptide	biosapiens	\N	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	44162	SO:0100009	\N	lipoprotein_signal_peptide	SO:0100009
0	"An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]	biosapiens	no_output	biosapiens	\N	sequence	"An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]	SO	44163	SO:0100010	\N	no_output	SO:0100010
0	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens,SOFA	cleaved_peptide_region	biosapiens,SOFA	\N	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	44164	SO:0100011	\N	cleaved_peptide_region	SO:0100011
0	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	biosapiens	peptide_coil	biosapiens	\N	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	44165	SO:0100012	\N	peptide_coil	SO:0100012
0	"Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]	biosapiens	hydrophobic_region_of_peptide	biosapiens	\N	sequence	"Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]	SO	44166	SO:0100013	\N	hydrophobic_region_of_peptide	SO:0100013
0	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	biosapiens	n_terminal_region	biosapiens	\N	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	44167	SO:0100014	\N	n_terminal_region	SO:0100014
0	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	biosapiens	c_terminal_region	biosapiens	\N	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	44168	SO:0100015	\N	c_terminal_region	SO:0100015
0	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	biosapiens	central_hydrophobic_region_of_signal_peptide	biosapiens	\N	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	44169	SO:0100016	\N	central_hydrophobic_region_of_signal_peptide	SO:0100016
0	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_motif	biosapiens	\N	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	44170	SO:0100017	\N	polypeptide_conserved_motif	SO:0100017
0	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	biosapiens	polypeptide_binding_motif	biosapiens	\N	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	44171	SO:0100018	\N	polypeptide_binding_motif	SO:0100018
0	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	biosapiens	polypeptide_catalytic_motif	biosapiens	\N	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	44172	SO:0100019	\N	polypeptide_catalytic_motif	SO:0100019
0	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	biosapiens	polypeptide_DNA_contact	biosapiens	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	44173	SO:0100020	\N	polypeptide_DNA_contact	SO:0100020
0	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	\N	sequence	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	44174	SO:0100021	\N	polypeptide_conserved_region	SO:0100021
0	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SOFA	substitution	SOFA	\N	sequence	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SO	44175	SO:1000002	\N	substitution	SO:1000002
0	"When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SOFA	complex_substitution	SOFA	\N	sequence	"When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	44176	SO:1000005	\N	complex_substitution	SO:1000005
0	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SOFA	point_mutation	SOFA	\N	sequence	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SO	44177	SO:1000008	\N	point_mutation	SO:1000008
0	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transition	\N	\N	sequence	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	44178	SO:1000009	\N	transition	SO:1000009
0	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	\N	pyrimidine_transition	\N	\N	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	44179	SO:1000010	\N	pyrimidine_transition	SO:1000010
0	"A transition of a cytidine to a thymine." [SO:ke]	\N	C_to_T_transition	\N	\N	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	44180	SO:1000011	\N	C_to_T_transition	SO:1000011
0	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	C_to_T_transition_at_pCpG_site	\N	\N	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	44181	SO:1000012	\N	C_to_T_transition_at_pCpG_site	SO:1000012
0	"" []	\N	T_to_C_transition	\N	\N	sequence	"" []	SO	44182	SO:1000013	\N	T_to_C_transition	SO:1000013
0	"A substitution of a purine, A or G, for another purine." [SO:ke]	\N	purine_transition	\N	\N	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	44183	SO:1000014	\N	purine_transition	SO:1000014
0	"A transition of an adenine to a guanine." [SO:ke]	\N	A_to_G_transition	\N	\N	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	44184	SO:1000015	\N	A_to_G_transition	SO:1000015
0	"A transition of a guanine to an adenine." [SO:ke]	\N	G_to_A_transition	\N	\N	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	44185	SO:1000016	\N	G_to_A_transition	SO:1000016
0	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	44186	SO:1000017	\N	transversion	SO:1000017
0	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	\N	pyrimidine_to_purine_transversion	\N	\N	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	44187	SO:1000018	\N	pyrimidine_to_purine_transversion	SO:1000018
0	"A transversion from cytidine to adenine." [SO:ke]	\N	C_to_A_transversion	\N	\N	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	44188	SO:1000019	\N	C_to_A_transversion	SO:1000019
0	"" []	\N	C_to_G_transversion	\N	\N	sequence	"" []	SO	44189	SO:1000020	\N	C_to_G_transversion	SO:1000020
0	"A transversion from T to A." [SO:ke]	\N	T_to_A_transversion	\N	\N	sequence	"A transversion from T to A." [SO:ke]	SO	44190	SO:1000021	\N	T_to_A_transversion	SO:1000021
0	"A transversion from T to G." [SO:ke]	\N	T_to_G_transversion	\N	\N	sequence	"A transversion from T to G." [SO:ke]	SO	44191	SO:1000022	\N	T_to_G_transversion	SO:1000022
0	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	\N	purine_to_pyrimidine_transversion	\N	\N	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	44192	SO:1000023	\N	purine_to_pyrimidine_transversion	SO:1000023
0	"A transversion from adenine to cytidine." [SO:ke]	\N	A_to_C_transversion	\N	\N	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	44193	SO:1000024	\N	A_to_C_transversion	SO:1000024
0	"A transversion from adenine to thymine." [SO:ke]	\N	A_to_T_transversion	\N	\N	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	44194	SO:1000025	\N	A_to_T_transversion	SO:1000025
0	"A transversion from guanine to cytidine." [SO:ke]	\N	G_to_C_transversion	\N	\N	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	44195	SO:1000026	\N	G_to_C_transversion	SO:1000026
0	"A transversion from guanine to thymine." [SO:ke]	\N	G_to_T_transversion	\N	\N	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	44196	SO:1000027	\N	G_to_T_transversion	SO:1000027
0	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	44197	SO:1000028	\N	intrachromosomal_mutation	SO:1000028
0	"An incomplete chromosome." [SO:ke]	\N	chromosomal_deletion	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	44198	SO:1000029	\N	chromosomal_deletion	SO:1000029
0	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	\N	chromosomal_inversion	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	44199	SO:1000030	\N	chromosomal_inversion	SO:1000030
0	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	44200	SO:1000031	\N	interchromosomal_mutation	SO:1000031
0	"A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel]	\N	indel	\N	\N	sequence	"A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel]	SO	44201	SO:1000032	\N	indel	SO:1000032
0	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	\N	duplication	\N	\N	sequence	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	SO	44202	SO:1000035	\N	duplication	SO:1000035
0	"A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	DBVAR,SOFA	inversion	DBVAR,SOFA	\N	sequence	"A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	44203	SO:1000036	\N	inversion	SO:1000036
0	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	44204	SO:1000037	\N	chromosomal_duplication	SO:1000037
0	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	44205	SO:1000038	\N	intrachromosomal_duplication	SO:1000038
0	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	\N	direct_tandem_duplication	\N	\N	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	44206	SO:1000039	\N	direct_tandem_duplication	SO:1000039
0	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	\N	inverted_tandem_duplication	\N	\N	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	44207	SO:1000040	\N	inverted_tandem_duplication	SO:1000040
0	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	\N	intrachromosomal_transposition	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	44208	SO:1000041	\N	intrachromosomal_transposition	SO:1000041
0	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	\N	compound_chromosome	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	44209	SO:1000042	\N	compound_chromosome	SO:1000042
0	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	\N	Robertsonian_fusion	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	44210	SO:1000043	\N	Robertsonian_fusion	SO:1000043
0	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	\N	chromosomal_translocation	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	44211	SO:1000044	\N	chromosomal_translocation	SO:1000044
0	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	\N	ring_chromosome	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	44212	SO:1000045	\N	ring_chromosome	SO:1000045
0	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	\N	pericentric_inversion	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	44213	SO:1000046	\N	pericentric_inversion	SO:1000046
0	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	\N	paracentric_inversion	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	44214	SO:1000047	\N	paracentric_inversion	SO:1000047
0	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	\N	reciprocal_chromosomal_translocation	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	44215	SO:1000048	\N	reciprocal_chromosomal_translocation	SO:1000048
0	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	\N	autosynaptic_chromosome	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	44216	SO:1000136	\N	autosynaptic_chromosome	SO:1000136
0	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	\N	homo_compound_chromosome	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	44217	SO:1000138	\N	homo_compound_chromosome	SO:1000138
0	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	\N	hetero_compound_chromosome	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	44218	SO:1000140	\N	hetero_compound_chromosome	SO:1000140
0	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	\N	chromosome_fission	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	44219	SO:1000141	\N	chromosome_fission	SO:1000141
0	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	\N	dexstrosynaptic_chromosome	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	44220	SO:1000142	\N	dexstrosynaptic_chromosome	SO:1000142
0	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	\N	laevosynaptic_chromosome	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	44221	SO:1000143	\N	laevosynaptic_chromosome	SO:1000143
0	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	\N	free_duplication	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	44222	SO:1000144	\N	free_duplication	SO:1000144
0	"A ring chromosome which is a copy of another chromosome." [SO:ke]	\N	free_ring_duplication	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	44223	SO:1000145	\N	free_ring_duplication	SO:1000145
0	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	\N	complex_chromosomal_mutation	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	44224	SO:1000146	\N	complex_chromosomal_mutation	SO:1000146
0	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	\N	deficient_translocation	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	44225	SO:1000147	\N	deficient_translocation	SO:1000147
0	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	\N	inversion_cum_translocation	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	44226	SO:1000148	\N	inversion_cum_translocation	SO:1000148
0	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	\N	bipartite_duplication	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	44227	SO:1000149	\N	bipartite_duplication	SO:1000149
0	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	\N	cyclic_translocation	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	44228	SO:1000150	\N	cyclic_translocation	SO:1000150
0	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	\N	bipartite_inversion	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	44229	SO:1000151	\N	bipartite_inversion	SO:1000151
0	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	\N	uninverted_insertional_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	44230	SO:1000152	\N	uninverted_insertional_duplication	SO:1000152
0	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	\N	inverted_insertional_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	44231	SO:1000153	\N	inverted_insertional_duplication	SO:1000153
0	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	\N	insertional_duplication	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	44232	SO:1000154	\N	insertional_duplication	SO:1000154
0	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	\N	interchromosomal_transposition	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	44233	SO:1000155	\N	interchromosomal_transposition	SO:1000155
0	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	\N	inverted_interchromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	44234	SO:1000156	\N	inverted_interchromosomal_transposition	SO:1000156
0	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	\N	uninverted_interchromosomal_transposition	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	44235	SO:1000157	\N	uninverted_interchromosomal_transposition	SO:1000157
0	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	\N	inverted_intrachromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	44236	SO:1000158	\N	inverted_intrachromosomal_transposition	SO:1000158
0	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	\N	uninverted_intrachromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	44237	SO:1000159	\N	uninverted_intrachromosomal_transposition	SO:1000159
0	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	\N	unoriented_insertional_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	44238	SO:1000160	\N	unoriented_insertional_duplication	SO:1000160
0	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	\N	unoriented_interchromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	44239	SO:1000161	\N	unoriented_interchromosomal_transposition	SO:1000161
0	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	\N	unoriented_intrachromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	44240	SO:1000162	\N	unoriented_intrachromosomal_transposition	SO:1000162
0	"" []	\N	uncharacterised_chromosomal_mutation	\N	\N	sequence	"" []	SO	44241	SO:1000170	\N	uncharacterised_chromosomal_mutation	SO:1000170
0	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	\N	deficient_inversion	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	44242	SO:1000171	\N	deficient_inversion	SO:1000171
0	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	DBVAR	tandem_duplication	DBVAR	\N	sequence	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	SO	44243	SO:1000173	\N	tandem_duplication	SO:1000173
0	"" []	\N	partially_characterised_chromosomal_mutation	\N	\N	sequence	"" []	SO	44244	SO:1000175	\N	partially_characterised_chromosomal_mutation	SO:1000175
0	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	chromosome_number_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	44245	SO:1000182	\N	chromosome_number_variation	SO:1000182
0	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"" []	SO	44246	SO:1000183	\N	chromosome_structure_variation	SO:1000183
0	"A transcript that is alternatively spliced." [SO:xp]	\N	alternatively_spliced_transcript	\N	\N	sequence	"A transcript that is alternatively spliced." [SO:xp]	SO	44247	SO:1001187	\N	alternatively_spliced_transcript	SO:1001187
0	"A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]	\N	encodes_1_polypeptide	\N	\N	sequence	"A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]	SO	44248	SO:1001188	\N	encodes_1_polypeptide	SO:1001188
0	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	\N	encodes_greater_than_1_polypeptide	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	SO	44249	SO:1001189	\N	encodes_greater_than_1_polypeptide	SO:1001189
0	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]	\N	encodes_different_polypeptides_different_stop	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]	SO	44250	SO:1001190	\N	encodes_different_polypeptides_different_stop	SO:1001190
0	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]	\N	encodes_overlapping_peptides_different_start	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]	SO	44251	SO:1001191	\N	encodes_overlapping_peptides_different_start	SO:1001191
0	"A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]	\N	encodes_disjoint_polypeptides	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]	SO	44252	SO:1001192	\N	encodes_disjoint_polypeptides	SO:1001192
0	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]	\N	encodes_overlapping_polypeptides_different_start_and_stop	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]	SO	44253	SO:1001193	\N	encodes_overlapping_polypeptides_different_start_and_stop	SO:1001193
0	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	\N	encodes_overlapping_peptides	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	SO	44254	SO:1001195	\N	encodes_overlapping_peptides	SO:1001195
0	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	\N	cryptogene	\N	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	44255	SO:1001196	\N	cryptogene	SO:1001196
0	"A primary transcript that has the quality dicistronic." [SO:xp]	\N	dicistronic_primary_transcript	\N	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	44256	SO:1001197	\N	dicistronic_primary_transcript	SO:1001197
0	"" []	\N	member_of_regulon	\N	\N	sequence	"" []	SO	44257	SO:1001217	\N	member_of_regulon	SO:1001217
0	"A CDS with the evidence status of being independently known." [SO:xp]	\N	CDS_independently_known	\N	\N	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	44258	SO:1001246	\N	CDS_independently_known	SO:1001246
0	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	\N	orphan_CDS	\N	\N	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	44259	SO:1001247	\N	orphan_CDS	SO:1001247
0	"A CDS that is supported by domain similarity." [SO:xp]	\N	CDS_supported_by_domain_match_data	\N	\N	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	44260	SO:1001249	\N	CDS_supported_by_domain_match_data	SO:1001249
0	"A CDS that is supported by sequence similarity data." [SO:xp]	\N	CDS_supported_by_sequence_similarity_data	\N	\N	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	44261	SO:1001251	\N	CDS_supported_by_sequence_similarity_data	SO:1001251
0	"A CDS that is predicted." [SO:ke]	\N	CDS_predicted	\N	\N	sequence	"A CDS that is predicted." [SO:ke]	SO	44262	SO:1001254	\N	CDS_predicted	SO:1001254
0	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	\N	CDS_supported_by_EST_or_cDNA_data	\N	\N	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	44263	SO:1001259	\N	CDS_supported_by_EST_or_cDNA_data	SO:1001259
0	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	\N	internal_Shine_Dalgarno_sequence	\N	\N	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	44264	SO:1001260	\N	internal_Shine_Dalgarno_sequence	SO:1001260
0	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	\N	recoded_mRNA	\N	\N	sequence	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	44265	SO:1001261	\N	recoded_mRNA	SO:1001261
0	"An attribute describing a translational frameshift of -1." [SO:ke]	\N	minus_1_translationally_frameshifted	\N	\N	sequence	"An attribute describing a translational frameshift of -1." [SO:ke]	SO	44266	SO:1001262	\N	minus_1_translationally_frameshifted	SO:1001262
0	"An attribute describing a translational frameshift of +1." [SO:ke]	\N	plus_1_translationally_frameshifted	\N	\N	sequence	"An attribute describing a translational frameshift of +1." [SO:ke]	SO	44267	SO:1001263	\N	plus_1_translationally_frameshifted	SO:1001263
0	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	\N	mRNA_recoded_by_translational_bypass	\N	\N	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	44268	SO:1001264	\N	mRNA_recoded_by_translational_bypass	SO:1001264
0	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	\N	mRNA_recoded_by_codon_redefinition	\N	\N	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	44269	SO:1001265	\N	mRNA_recoded_by_codon_redefinition	SO:1001265
0	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	44270	SO:1001268	\N	recoding_stimulatory_region	SO:1001268
0	"A non-canonical start codon with 4 base pairs." [SO:ke]	\N	four_bp_start_codon	\N	\N	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	44271	SO:1001269	\N	four_bp_start_codon	SO:1001269
0	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	\N	archaeal_intron	\N	\N	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	44272	SO:1001271	\N	archaeal_intron	SO:1001271
0	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	\N	tRNA_intron	\N	\N	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	44273	SO:1001272	\N	tRNA_intron	SO:1001272
0	"A non-canonical start codon of sequence CTG." [SO:ke]	\N	CTG_start_codon	\N	\N	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	44274	SO:1001273	\N	CTG_start_codon	SO:1001273
0	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	\N	SECIS_element	\N	\N	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	44275	SO:1001274	\N	SECIS_element	SO:1001274
0	"Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]	\N	retron	\N	\N	sequence	"Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]	SO	44276	SO:1001275	\N	retron	SO:1001275
0	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	\N	three_prime_recoding_site	\N	\N	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	44277	SO:1001277	\N	three_prime_recoding_site	SO:1001277
0	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	\N	three_prime_stem_loop_structure	\N	\N	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	44278	SO:1001279	\N	three_prime_stem_loop_structure	SO:1001279
0	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	\N	five_prime_recoding_site	\N	\N	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	44279	SO:1001280	\N	five_prime_recoding_site	SO:1001280
0	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	\N	flanking_three_prime_quadruplet_recoding_signal	\N	\N	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	44280	SO:1001281	\N	flanking_three_prime_quadruplet_recoding_signal	SO:1001281
0	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	\N	UAG_stop_codon_signal	\N	\N	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	44281	SO:1001282	\N	UAG_stop_codon_signal	SO:1001282
0	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	\N	UAA_stop_codon_signal	\N	\N	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	44282	SO:1001283	\N	UAA_stop_codon_signal	SO:1001283
0	"A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]	SOFA	regulon	SOFA	\N	sequence	"A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]	SO	44283	SO:1001284	\N	regulon	SO:1001284
0	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	\N	UGA_stop_codon_signal	\N	\N	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	44284	SO:1001285	\N	UGA_stop_codon_signal	SO:1001285
0	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	\N	three_prime_repeat_recoding_signal	\N	\N	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	44285	SO:1001286	\N	three_prime_repeat_recoding_signal	SO:1001286
0	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	\N	distant_three_prime_recoding_signal	\N	\N	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	44286	SO:1001287	\N	distant_three_prime_recoding_signal	SO:1001287
0	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	\N	stop_codon_signal	\N	\N	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	44287	SO:1001288	\N	stop_codon_signal	SO:1001288
0	"The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]	SOFA	databank_entry	SOFA	\N	sequence	"The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]	SO	44288	SO:2000061	\N	databank_entry	SO:2000061
0	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	\N	gene_segment	\N	\N	sequence	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	SO	44289	SO:3000000	\N	gene_segment	SO:3000000
1	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SO	185520	SO:0000001	SO:0000001	region	SO:0000110
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A folded sequence." [SO:ke]	SO	185521	SO:0000002	SO:0000002	sequence_secondary_structure	SO:0001411
1	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]	SO	185522	SO:0000003	SO:0000003	G_quartet	SO:0000002
1	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SOFA	coding_exon	SOFA	SOFA	sequence	"" []	SO	185523	SO:0000004	SO:0000004	interior_coding_exon	SO:0000195
1	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SOFA	tandem_repeat	SOFA	SOFA	sequence	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185524	SO:0000005	SO:0000005	satellite_DNA	SO:0000705
1	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A region amplified by a PCR reaction." [SO:ke]	SO	185525	SO:0000006	SO:0000006	PCR_product	SO:0000695
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SOFA	read	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	185526	SO:0000007	SO:0000007	read_pair	SO:0000150
1	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SOFA	contig	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	185527	SO:0000007	SO:0000007	read_pair	SO:0000149
1	"An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]	SOFA	paired_end_fragment	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	185528	SO:0000007	SO:0000007	read_pair	SO:0001790
1	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	185529	SO:0000010	SO:0000010	protein_coding	SO:0000401
1	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	185530	SO:0000011	SO:0000011	non_protein_coding	SO:0000401
1	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	SO	185531	SO:0000012	SO:0000012	scRNA_primary_transcript	SO:0000483
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SO	185532	SO:0000013	SO:0000013	scRNA	SO:0000655
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	185533	SO:0000014	SO:0000014	INR_motif	SO:0001660
1	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	185534	SO:0000014	SO:0000014	INR_motif	SO:0001669
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	185535	SO:0000015	SO:0000015	DPE_motif	SO:0001660
1	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	185536	SO:0000015	SO:0000015	DPE_motif	SO:0001669
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	185537	SO:0000016	SO:0000016	BREu_motif	SO:0001660
1	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	185538	SO:0000016	SO:0000016	BREu_motif	SO:0001669
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	185539	SO:0000017	SO:0000017	PSE_motif	SO:0000713
1	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	185540	SO:0000017	SO:0000017	PSE_motif	SO:0000167
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]	SO	185541	SO:0000018	SO:0000018	linkage_group	SO:0001411
1	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	SO	185542	SO:0000020	SO:0000020	RNA_internal_loop	SO:0000715
1	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	\N	RNA_internal_loop	\N	\N	sequence	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	SO	185543	SO:0000021	SO:0000021	asymmetric_RNA_internal_loop	SO:0000020
1	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]	SO	185544	SO:0000022	SO:0000022	A_minor_RNA_motif	SO:0000715
1	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	\N	asymmetric_RNA_internal_loop	\N	\N	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	185545	SO:0000023	SO:0000023	K_turn_RNA_motif	SO:0000021
1	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	\N	asymmetric_RNA_internal_loop	\N	\N	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	185546	SO:0000024	SO:0000024	sarcin_like_RNA_motif	SO:0000021
1	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	\N	RNA_internal_loop	\N	\N	sequence	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	SO	185547	SO:0000025	SO:0000025	symmetric_RNA_internal_loop	SO:0000020
1	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"" []	SO	185548	SO:0000026	SO:0000026	RNA_junction_loop	SO:0000715
1	"" []	\N	RNA_junction_loop	\N	\N	sequence	"" []	SO	185549	SO:0000027	SO:0000027	RNA_hook_turn	SO:0000026
1	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"" []	SO	185550	SO:0000028	SO:0000028	base_pair	SO:0000002
1	"" []	\N	base_pair	\N	\N	sequence	"The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]	SO	185551	SO:0000029	SO:0000029	WC_base_pair	SO:0000028
1	"" []	\N	base_pair	\N	\N	sequence	"A type of non-canonical base-pairing." [PMID:12177293]	SO	185552	SO:0000030	SO:0000030	sugar_edge_base_pair	SO:0000028
1	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	185553	SO:0000031	SO:0000031	aptamer	SO:0000696
1	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	\N	aptamer	\N	\N	sequence	"DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]	SO	185554	SO:0000032	SO:0000032	DNA_aptamer	SO:0000031
1	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	\N	aptamer	\N	\N	sequence	"RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	185555	SO:0000033	SO:0000033	RNA_aptamer	SO:0000031
1	"An oligo composed of synthetic nucleotides." [SO:ke]	\N	synthetic_oligo	\N	\N	sequence	"Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]	SO	185556	SO:0000034	SO:0000034	morpholino_oligo	SO:0001247
1	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	185557	SO:0000035	SO:0000035	riboswitch	SO:0000836
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	185558	SO:0000035	SO:0000035	riboswitch	SO:0000234
1	"" []	\N	chromosomal_regulatory_element	\N	\N	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	185559	SO:0000036	SO:0000036	matrix_attachment_site	SO:0000626
1	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	\N	CRM	SOFA	\N	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	185560	SO:0000037	SO:0000037	locus_control_region	SO:0000727
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A part of a match, for example an hsp from blast is a match_part." [SO:ke]	SO	185561	SO:0000039	SO:0000039	match_part	SO:0001410
1	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	SOFA	sequence	"A part of a match, for example an hsp from blast is a match_part." [SO:ke]	SO	185562	SO:0000039	SO:0000039	match_part	SO:0000343
1	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A clone of a DNA region of a genome." [SO:ma]	SO	185563	SO:0000040	SO:0000040	genomic_clone	SO:0000151
1	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]	SO	185564	SO:0000043	SO:0000043	processed_pseudogene	SO:0000336
1	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	\N	non_processed_pseudogene	\N	\N	sequence	"A pseudogene caused by unequal crossing over at recombination." [SO:ke]	SO	185565	SO:0000044	SO:0000044	pseudogene_by_unequal_crossing_over	SO:0001760
1	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	SO	185566	SO:0000051	SO:0000051	probe	SO:0000696
1	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	chromosome_number_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	185567	SO:0000054	SO:0000054	aneuploid	SO:1000182
1	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	aneuploid	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	185568	SO:0000055	SO:0000055	hyperploid	SO:0000054
1	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	aneuploid	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	185569	SO:0000056	SO:0000056	hypoploid	SO:0000054
1	"" []	SOFA	gene_group_regulatory_region	SOFA	SOFA	sequence	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SO	185570	SO:0000057	SO:0000057	operator	SO:0000752
1	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SOFA	nucleotide_to_protein_binding_site	SOFA	SOFA	sequence	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SO	185571	SO:0000059	SO:0000059	nuclease_binding_site	SO:0001654
1	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	\N	compound_chromosome	\N	\N	sequence	"" []	SO	185572	SO:0000060	SO:0000060	compound_chromosome_arm	SO:1000042
1	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	\N	nuclease_binding_site	SOFA	\N	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	SO	185573	SO:0000061	SO:0000061	restriction_enzyme_binding_site	SO:0000059
1	"An incomplete chromosome." [SO:ke]	\N	chromosomal_deletion	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	185574	SO:0000062	SO:0000062	deficient_intrachromosomal_transposition	SO:1000029
1	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	\N	intrachromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	185575	SO:0000062	SO:0000062	deficient_intrachromosomal_transposition	SO:1000041
1	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	\N	interchromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	185576	SO:0000063	SO:0000063	deficient_interchromosomal_transposition	SO:1000155
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	185577	SO:0000065	SO:0000065	free_chromosome_arm	SO:1000183
1	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	185578	SO:0000067	SO:0000067	gene_to_gene_feature	SO:0000401
1	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	SO	185579	SO:0000068	SO:0000068	overlapping	SO:0000067
1	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	SO	185580	SO:0000069	SO:0000069	inside_intron	SO:0000068
1	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	\N	inside_intron	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]	SO	185581	SO:0000070	SO:0000070	inside_intron_antiparallel	SO:0000069
1	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	\N	inside_intron	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]	SO	185582	SO:0000071	SO:0000071	inside_intron_parallel	SO:0000069
1	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]	SO	185583	SO:0000073	SO:0000073	five_prime_three_prime_overlap	SO:0000068
1	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]	SO	185584	SO:0000074	SO:0000074	five_prime_five_prime_overlap	SO:0000068
1	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]	SO	185585	SO:0000075	SO:0000075	three_prime_three_prime_overlap	SO:0000068
1	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]	SO	185586	SO:0000076	SO:0000076	three_prime_five_prime_overlap	SO:0000068
1	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]	SO	185587	SO:0000077	SO:0000077	antisense	SO:0000068
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is polycistronic." [SO:xp]	SO	185588	SO:0000078	SO:0000078	polycistronic_transcript	SO:0000673
1	"A transcript that is polycistronic." [SO:xp]	\N	polycistronic_transcript	\N	\N	sequence	"A transcript that is dicistronic." [SO:ke]	SO	185589	SO:0000079	SO:0000079	dicistronic_transcript	SO:0000078
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is dicistronic." [SO:ke]	SO	185590	SO:0000079	SO:0000079	dicistronic_transcript	SO:0000673
1	"" []	\N	gene_array_member	\N	\N	sequence	"" []	SO	185591	SO:0000080	SO:0000080	operon_member	SO:0000081
1	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	185592	SO:0000081	SO:0000081	gene_array_member	SO:0000401
1	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	185593	SO:0000083	SO:0000083	macronuclear_sequence	SO:0000736
1	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	185594	SO:0000084	SO:0000084	micronuclear_sequence	SO:0000736
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from nuclear sequence." [SO:xp]	SO	185595	SO:0000087	SO:0000087	nuclear_gene	SO:0000704
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene located in mitochondrial sequence." [SO:xp]	SO	185596	SO:0000088	SO:0000088	mt_gene	SO:0000704
1	"A gene located in mitochondrial sequence." [SO:xp]	\N	mt_gene	\N	\N	sequence	"A gene located in kinetoplast sequence." [SO:xp]	SO	185597	SO:0000089	SO:0000089	kinetoplast_gene	SO:0000088
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from plastid sequence." [SO:xp]	SO	185598	SO:0000090	SO:0000090	plastid_gene	SO:0000704
1	"A gene from plastid sequence." [SO:xp]	\N	plastid_gene	\N	\N	sequence	"A gene from apicoplast sequence." [SO:xp]	SO	185599	SO:0000091	SO:0000091	apicoplast_gene	SO:0000090
1	"A gene from plastid sequence." [SO:xp]	\N	plastid_gene	\N	\N	sequence	"A gene from chloroplast sequence." [SO:xp]	SO	185600	SO:0000092	SO:0000092	ct_gene	SO:0000090
1	"A gene from plastid sequence." [SO:xp]	\N	plastid_gene	\N	\N	sequence	"A gene from chromoplast_sequence." [SO:xp]	SO	185601	SO:0000093	SO:0000093	chromoplast_gene	SO:0000090
1	"A gene from plastid sequence." [SO:xp]	\N	plastid_gene	\N	\N	sequence	"A gene from cyanelle sequence." [SO:xp]	SO	185602	SO:0000094	SO:0000094	cyanelle_gene	SO:0000090
1	"A gene from plastid sequence." [SO:xp]	\N	plastid_gene	\N	\N	sequence	"A plastid gene from leucoplast sequence." [SO:xp]	SO	185603	SO:0000095	SO:0000095	leucoplast_gene	SO:0000090
1	"A gene from plastid sequence." [SO:xp]	\N	plastid_gene	\N	\N	sequence	"A gene from proplastid sequence." [SO:ke]	SO	185604	SO:0000096	SO:0000096	proplastid_gene	SO:0000090
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from nucleomorph sequence." [SO:xp]	SO	185605	SO:0000097	SO:0000097	nucleomorph_gene	SO:0000704
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from plasmid sequence." [SO:xp]	SO	185606	SO:0000098	SO:0000098	plasmid_gene	SO:0000704
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from proviral sequence." [SO:xp]	SO	185607	SO:0000099	SO:0000099	proviral_gene	SO:0000704
1	"A gene from proviral sequence." [SO:xp]	\N	proviral_gene	\N	\N	sequence	"A proviral gene with origin endogenous retrovirus." [SO:xp]	SO	185608	SO:0000100	SO:0000100	endogenous_retroviral_gene	SO:0000099
1	"An MGE that is integrated into the host chromosome." [SO:ke]	SOFA	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	SO	185609	SO:0000101	SO:0000101	transposable_element	SO:0001039
1	"A match against a nucleotide sequence." [SO:ke]	SOFA	nucleotide_match	SOFA	SOFA	sequence	"A match to an EST or cDNA sequence." [SO:ke]	SO	185610	SO:0000102	SO:0000102	expressed_sequence_match	SO:0000347
1	"A sequence_feature with an extent of zero." [SO:ke]	SOFA	junction	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	185611	SO:0000103	SO:0000103	clone_insert_end	SO:0000699
1	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SOFA	clone_insert	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	185612	SO:0000103	SO:0000103	clone_insert_end	SO:0000753
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	SO	185613	SO:0000104	SO:0000104	polypeptide	SO:0001411
1	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	\N	sequence	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	SO	185614	SO:0000105	SO:0000105	chromosome_arm	SO:0000830
1	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	\N	primer	SOFA	\N	sequence	"" []	SO	185615	SO:0000107	SO:0000107	sequencing_primer	SO:0000112
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA with a frameshift." [SO:xp]	SO	185616	SO:0000108	SO:0000108	mRNA_with_frameshift	SO:0000234
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	185617	SO:0000111	SO:0000111	transposable_element_gene	SO:0000704
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	185618	SO:0000111	SO:0000111	transposable_element_gene	SO:0000101
1	"A single stranded oligonucleotide." [SO:ke]	SOFA	ss_oligo	SOFA	SOFA	sequence	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	SO	185619	SO:0000112	SO:0000112	primer	SO:0000441
1	"An MGE that is integrated into the host chromosome." [SO:ke]	SOFA	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A viral sequence which has integrated into a host genome." [SO:ke]	SO	185620	SO:0000113	SO:0000113	proviral_region	SO:0001039
1	"A nucleotide modified by methylation." [SO:ke]	SOFA	methylated_DNA_base_feature	SOFA	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	185621	SO:0000114	SO:0000114	methylated_cytosine	SO:0000306
1	"A modified cytosine DNA base feature." [SO:ke]	SOFA	modified_cytosine	\N	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	185622	SO:0000114	SO:0000114	methylated_cytosine	SO:0001963
1	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a sequence that is modified by editing." [SO:ke]	SO	185623	SO:0000116	SO:0000116	edited	SO:0000237
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript with a translational frameshift." [SO:xp]	SO	185624	SO:0000118	SO:0000118	transcript_with_translational_frameshift	SO:0000673
1	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe a sequence that is regulated." [SO:ke]	SO	185625	SO:0000119	SO:0000119	regulated	SO:0000401
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	SO	185626	SO:0000120	SO:0000120	protein_coding_primary_transcript	SO:0000185
1	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	\N	primer	SOFA	\N	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	185627	SO:0000121	SO:0000121	forward_primer	SO:0000112
1	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A folded RNA sequence." [SO:ke]	SO	185628	SO:0000122	SO:0000122	RNA_sequence_secondary_structure	SO:0000002
1	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing a gene that is regulated at transcription." [SO:ma]	SO	185629	SO:0000123	SO:0000123	transcriptionally_regulated	SO:0000119
1	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]	SO	185630	SO:0000124	SO:0000124	transcriptionally_constitutive	SO:0000123
1	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An inducer molecule is required for transcription to occur." [SO:ke]	SO	185631	SO:0000125	SO:0000125	transcriptionally_induced	SO:0000123
1	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"A repressor molecule is required for transcription to stop." [SO:ke]	SO	185632	SO:0000126	SO:0000126	transcriptionally_repressed	SO:0000123
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced." [SO:xp]	SO	185633	SO:0000127	SO:0000127	silenced_gene	SO:0000704
1	"A gene that is silenced." [SO:xp]	\N	silenced_gene	\N	\N	sequence	"A gene that is silenced by DNA modification." [SO:xp]	SO	185634	SO:0000128	SO:0000128	gene_silenced_by_DNA_modification	SO:0000127
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced by DNA modification." [SO:xp]	SO	185635	SO:0000128	SO:0000128	gene_silenced_by_DNA_modification	SO:0000704
1	"A gene that is silenced by DNA modification." [SO:xp]	\N	gene_silenced_by_DNA_modification	\N	\N	sequence	"A gene that is silenced by DNA methylation." [SO:xp]	SO	185636	SO:0000129	SO:0000129	gene_silenced_by_DNA_methylation	SO:0000128
1	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing a gene that is regulated after it has been translated." [SO:ke]	SO	185637	SO:0000130	SO:0000130	post_translationally_regulated	SO:0000119
1	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing a gene that is regulated as it is translated." [SO:ke]	SO	185638	SO:0000131	SO:0000131	translationally_regulated	SO:0000119
1	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	\N	primer	SOFA	\N	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	185639	SO:0000132	SO:0000132	reverse_primer	SO:0000112
1	"" []	\N	gene_attribute	\N	\N	sequence	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	SO	185640	SO:0000133	SO:0000133	epigenetically_modified	SO:0000401
1	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	SO	185641	SO:0000134	SO:0000134	genomically_imprinted	SO:0000119
1	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	\N	epigenetically_modified	\N	\N	sequence	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	SO	185642	SO:0000134	SO:0000134	genomically_imprinted	SO:0000133
1	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	\N	genomically_imprinted	\N	\N	sequence	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	185643	SO:0000135	SO:0000135	maternally_imprinted	SO:0000134
1	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	\N	genomically_imprinted	\N	\N	sequence	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	185644	SO:0000136	SO:0000136	paternally_imprinted	SO:0000134
1	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	\N	epigenetically_modified	\N	\N	sequence	"Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]	SO	185645	SO:0000137	SO:0000137	allelically_excluded	SO:0000133
1	"A gene that is epigenetically modified." [SO:ke]	\N	epigenetically_modified_gene	\N	\N	sequence	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	SO	185646	SO:0000138	SO:0000138	gene_rearranged_at_DNA_level	SO:0000898
1	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	185647	SO:0000139	SO:0000139	ribosome_entry_site	SO:0000836
1	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	five_prime_UTR	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	185648	SO:0000139	SO:0000139	ribosome_entry_site	SO:0000204
1	"A regulatory region that is involved in the control of the process of translation." [SO:ke]	SOFA	translation_regulatory_region	\N	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	185649	SO:0000140	SO:0000140	attenuator	SO:0001680
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	185650	SO:0000140	SO:0000140	attenuator	SO:0000234
1	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185651	SO:0000141	SO:0000141	terminator	SO:0001679
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185652	SO:0000141	SO:0000141	terminator	SO:0000673
1	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A folded DNA sequence." [SO:ke]	SO	185653	SO:0000142	SO:0000142	DNA_sequence_secondary_structure	SO:0000002
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SO	185654	SO:0000143	SO:0000143	assembly_component	SO:0001410
1	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	\N	codon	SOFA	\N	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	185655	SO:0000145	SO:0000145	recoded_codon	SO:0000360
1	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke]	SO	185656	SO:0000146	SO:0000146	capped	SO:0000237
1	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SO	185657	SO:0000147	SO:0000147	exon	SO:0000833
1	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	185658	SO:0000148	SO:0000148	supercontig	SO:0001876
1	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SOFA	ultracontig	SOFA	SOFA	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	185659	SO:0000148	SO:0000148	supercontig	SO:0000719
1	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	185660	SO:0000149	SO:0000149	contig	SO:0000143
1	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	185661	SO:0000149	SO:0000149	contig	SO:0000353
1	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SOFA	supercontig	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	185662	SO:0000149	SO:0000149	contig	SO:0000148
1	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	185663	SO:0000150	SO:0000150	read	SO:0000143
1	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SOFA	contig	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	185664	SO:0000150	SO:0000150	read	SO:0000149
1	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SO	185665	SO:0000151	SO:0000151	clone	SO:0000695
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	185666	SO:0000152	SO:0000152	YAC	SO:0000440
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	185667	SO:0000153	SO:0000153	BAC	SO:0000440
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	185668	SO:0000154	SO:0000154	PAC	SO:0000440
1	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	SO	185669	SO:0000155	SO:0000155	plasmid	SO:0001235
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	185670	SO:0000156	SO:0000156	cosmid	SO:0000440
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	185671	SO:0000157	SO:0000157	phagemid	SO:0000440
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	185672	SO:0000158	SO:0000158	fosmid	SO:0000440
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SOFA	sequence_alteration	SOFA	SOFA	sequence	"The point at which one or more contiguous nucleotides were excised." [SO:ke]	SO	185673	SO:0000159	SO:0000159	deletion	SO:0001059
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The point at which one or more contiguous nucleotides were excised." [SO:ke]	SO	185674	SO:0000159	SO:0000159	deletion	SO:0001411
1	"A nucleotide modified by methylation." [SO:ke]	SOFA	methylated_DNA_base_feature	SOFA	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	185675	SO:0000161	SO:0000161	methylated_adenine	SO:0000306
1	"A modified adenine DNA base feature." [SO:ke]	SOFA	modified_adenine	\N	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	185676	SO:0000161	SO:0000161	methylated_adenine	SO:0001962
1	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	185677	SO:0000162	SO:0000162	splice_site	SO:0000835
1	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SOFA	cis_splice_site	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	185678	SO:0000163	SO:0000163	five_prime_cis_splice_site	SO:0001419
1	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SOFA	cis_splice_site	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	185679	SO:0000164	SO:0000164	three_prime_cis_splice_site	SO:0001419
1	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SOFA	CRM	SOFA	SOFA	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185680	SO:0000165	SO:0000165	enhancer	SO:0000727
1	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	enhancer	SOFA	\N	sequence	"An enhancer bound by a factor." [SO:xp]	SO	185681	SO:0000166	SO:0000166	enhancer_bound_by_factor	SO:0000165
1	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SOFA	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SO	185682	SO:0000167	SO:0000167	promoter	SO:0001055
1	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	185683	SO:0000169	SO:0000169	RNApol_I_promoter	SO:0001203
1	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	185684	SO:0000170	SO:0000170	RNApol_II_promoter	SO:0001203
1	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	185685	SO:0000171	SO:0000171	RNApol_III_promoter	SO:0001203
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185686	SO:0000172	SO:0000172	CAAT_signal	SO:0000713
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185687	SO:0000172	SO:0000172	CAAT_signal	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185688	SO:0000173	SO:0000173	GC_rich_promoter_region	SO:0001659
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185689	SO:0000173	SO:0000173	GC_rich_promoter_region	SO:0000170
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	185690	SO:0000174	SO:0000174	TATA_box	SO:0001660
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185691	SO:0000175	SO:0000175	minus_10_signal	SO:0000713
1	"" []	\N	bacterial_RNApol_promoter_sigma_70	\N	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185692	SO:0000175	SO:0000175	minus_10_signal	SO:0001671
1	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	\N	bacterial_RNApol_promoter_sigma_ecf	\N	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185693	SO:0000175	SO:0000175	minus_10_signal	SO:0001913
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185694	SO:0000176	SO:0000176	minus_35_signal	SO:0000713
1	"" []	\N	bacterial_RNApol_promoter_sigma_70	\N	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185695	SO:0000176	SO:0000176	minus_35_signal	SO:0001671
1	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	\N	bacterial_RNApol_promoter_sigma_ecf	\N	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185696	SO:0000176	SO:0000176	minus_35_signal	SO:0001913
1	"A match against a nucleotide sequence." [SO:ke]	SOFA	nucleotide_match	SOFA	SOFA	sequence	"A nucleotide match against a sequence from another organism." [SO:ma]	SO	185697	SO:0000177	SO:0000177	cross_genome_match	SO:0000347
1	"A collection of related genes." [SO:ma]	SOFA	gene_group	SOFA	SOFA	sequence	"A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]	SO	185698	SO:0000178	SO:0000178	operon	SO:0005855
1	"A sequence_feature with an extent of zero." [SO:ke]	SOFA	junction	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	185699	SO:0000179	SO:0000179	clone_insert_start	SO:0000699
1	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SOFA	clone_insert	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	185700	SO:0000179	SO:0000179	clone_insert_start	SO:0000753
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	SO	185701	SO:0000180	SO:0000180	retrotransposon	SO:0000101
1	"A match against a nucleotide sequence." [SO:ke]	SOFA	nucleotide_match	SOFA	SOFA	sequence	"A match against a translated sequence." [SO:ke]	SO	185702	SO:0000181	SO:0000181	translated_nucleotide_match	SO:0000347
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	SO	185703	SO:0000182	SO:0000182	DNA_transposon	SO:0000101
1	"" []	SOFA	gene_component_region	SOFA	SOFA	sequence	"A region of the gene which is not transcribed." [SO:ke]	SO	185704	SO:0000183	SO:0000183	non_transcribed_region	SO:0000842
1	"An intron which is spliced by the spliceosome." [SO:ke]	\N	spliceosomal_intron	SOFA	\N	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	185705	SO:0000184	SO:0000184	U2_intron	SO:0000662
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SO	185706	SO:0000185	SO:0000185	primary_transcript	SO:0000673
1	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	185707	SO:0000186	SO:0000186	LTR_retrotransposon	SO:0000180
1	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185708	SO:0000188	SO:0000188	intron	SO:0000835
1	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	185709	SO:0000189	SO:0000189	non_LTR_retrotransposon	SO:0000180
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"" []	SO	185710	SO:0000190	SO:0000190	five_prime_intron	SO:0000188
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"" []	SO	185711	SO:0000191	SO:0000191	interior_intron	SO:0000188
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"" []	SO	185712	SO:0000192	SO:0000192	three_prime_intron	SO:0000188
1	"A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]	SOFA	restriction_fragment	SOFA	SOFA	sequence	"A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]	SO	185713	SO:0000193	SO:0000193	RFLP_fragment	SO:0000412
1	"A retrotransposon without long terminal repeat sequences." [SO:ke]	\N	non_LTR_retrotransposon	\N	\N	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	185714	SO:0000194	SO:0000194	LINE_element	SO:0000189
1	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	185715	SO:0000195	SO:0000195	coding_exon	SO:0000147
1	"The region of an exon that encodes for protein sequence." [SO:ke]	SOFA	coding_region_of_exon	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	185716	SO:0000196	SO:0000196	five_prime_coding_exon_coding_region	SO:0001215
1	"The 5' most coding exon." [SO:ke]	SOFA	five_prime_coding_exon	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	185717	SO:0000196	SO:0000196	five_prime_coding_exon_coding_region	SO:0000200
1	"The region of an exon that encodes for protein sequence." [SO:ke]	SOFA	coding_region_of_exon	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	185718	SO:0000197	SO:0000197	three_prime_coding_exon_coding_region	SO:0001215
1	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SOFA	three_prime_coding_exon	\N	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	185719	SO:0000197	SO:0000197	three_prime_coding_exon_coding_region	SO:0000202
1	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"An exon that does not contain any codons." [SO:ke]	SO	185720	SO:0000198	SO:0000198	noncoding_exon	SO:0000147
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR	sequence_alteration	SOFA	DBVAR	sequence	"A region of nucleotide sequence that has translocated to a new position." [SO:ke]	SO	185721	SO:0000199	SO:0000199	translocation	SO:0001059
1	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SOFA	coding_exon	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	185722	SO:0000200	SO:0000200	five_prime_coding_exon	SO:0000195
1	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	\N	exon	SOFA	\N	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	185723	SO:0000201	SO:0000201	interior_exon	SO:0000147
1	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	\N	coding_exon	SOFA	\N	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	185724	SO:0000202	SO:0000202	three_prime_coding_exon	SO:0000195
1	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	185725	SO:0000203	SO:0000203	UTR	SO:0000836
1	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SOFA	UTR	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185726	SO:0000204	SO:0000204	five_prime_UTR	SO:0000203
1	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SOFA	UTR	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185727	SO:0000205	SO:0000205	three_prime_UTR	SO:0000203
1	"A retrotransposon without long terminal repeat sequences." [SO:ke]	\N	non_LTR_retrotransposon	\N	\N	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	185728	SO:0000206	SO:0000206	SINE_element	SO:0000189
1	"" []	\N	sequence_length_variation	\N	\N	sequence	"" []	SO	185729	SO:0000207	SO:0000207	simple_sequence_length_variation	SO:0000248
1	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	185730	SO:0000208	SO:0000208	terminal_inverted_repeat_element	SO:0000182
1	"A primary transcript that is never translated into a protein." [SO:ke]	SOFA	nc_primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SO	185731	SO:0000209	SO:0000209	rRNA_primary_transcript	SO:0000483
1	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	SO	185732	SO:0000210	SO:0000210	tRNA_primary_transcript	SO:0000483
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	185733	SO:0000211	SO:0000211	alanine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	185734	SO:0000212	SO:0000212	arginine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	185735	SO:0000213	SO:0000213	asparagine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	185736	SO:0000214	SO:0000214	aspartic_acid_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	185737	SO:0000215	SO:0000215	cysteine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	185738	SO:0000216	SO:0000216	glutamic_acid_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	185739	SO:0000217	SO:0000217	glutamine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	185740	SO:0000218	SO:0000218	glycine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	185741	SO:0000219	SO:0000219	histidine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	185742	SO:0000220	SO:0000220	isoleucine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	185743	SO:0000221	SO:0000221	leucine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	185744	SO:0000222	SO:0000222	lysine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	185745	SO:0000223	SO:0000223	methionine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	185746	SO:0000224	SO:0000224	phenylalanine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	185747	SO:0000225	SO:0000225	proline_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	185748	SO:0000226	SO:0000226	serine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	185749	SO:0000227	SO:0000227	threonine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	185750	SO:0000228	SO:0000228	tryptophan_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	185751	SO:0000229	SO:0000229	tyrosine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	185752	SO:0000230	SO:0000230	valine_tRNA_primary_transcript	SO:0000210
1	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	SO	185753	SO:0000231	SO:0000231	snRNA_primary_transcript	SO:0000483
1	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	SO	185754	SO:0000232	SO:0000232	snoRNA_primary_transcript	SO:0000483
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SO	185755	SO:0000233	SO:0000233	mature_transcript	SO:0000673
1	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SO	185756	SO:0000234	SO:0000234	mRNA	SO:0000233
1	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SOFA	nucleotide_to_protein_binding_site	SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	185757	SO:0000235	SO:0000235	TF_binding_site	SO:0001654
1	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	185758	SO:0000235	SO:0000235	TF_binding_site	SO:0001679
1	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	SOFA	reading_frame	SOFA	SOFA	sequence	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	SO	185759	SO:0000236	SO:0000236	ORF	SO:0000717
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	185760	SO:0000237	SO:0000237	transcript_attribute	SO:0000733
1	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	185761	SO:0000238	SO:0000238	foldback_element	SO:0000182
1	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	SOFA	topologically_defined_region	SOFA	SOFA	sequence	"The sequences extending on either side of a specific region." [SO:ke]	SO	185762	SO:0000239	SO:0000239	flanking_region	SO:0001412
1	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"" []	SO	185763	SO:0000240	SO:0000240	chromosome_variation	SO:0001507
1	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"" []	SO	185764	SO:0000240	SO:0000240	chromosome_variation	SO:0001524
1	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	\N	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	185765	SO:0000241	SO:0000241	internal_UTR	SO:0000203
1	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	\N	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	185766	SO:0000242	SO:0000242	untranslated_region_polycistronic_mRNA	SO:0000203
1	"Region in mRNA where ribosome assembles." [SO:ke]	\N	ribosome_entry_site	SOFA	\N	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	185767	SO:0000243	SO:0000243	internal_ribosome_entry_site	SO:0000139
1	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]	SO	185768	SO:0000246	SO:0000246	polyadenylated	SO:0000863
1	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	\N	sequence	"" []	SO	185769	SO:0000248	SO:0000248	sequence_length_variation	SO:1000002
1	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A post_transcriptionally modified base." [SO:ke]	SO	185770	SO:0000250	SO:0000250	modified_RNA_base_feature	SO:0001236
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SO	185771	SO:0000252	SO:0000252	rRNA	SO:0000655
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SO	185772	SO:0000253	SO:0000253	tRNA	SO:0000655
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	185773	SO:0000254	SO:0000254	alanyl_tRNA	SO:0000253
1	"A primary transcript encoding a ribosomal RNA." [SO:ke]	\N	rRNA_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	185774	SO:0000255	SO:0000255	rRNA_small_subunit_primary_transcript	SO:0000209
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	185775	SO:0000256	SO:0000256	asparaginyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	185776	SO:0000257	SO:0000257	aspartyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	185777	SO:0000258	SO:0000258	cysteinyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	185778	SO:0000259	SO:0000259	glutaminyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	185779	SO:0000260	SO:0000260	glutamyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	185780	SO:0000261	SO:0000261	glycyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	185781	SO:0000262	SO:0000262	histidyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	185782	SO:0000263	SO:0000263	isoleucyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	185783	SO:0000264	SO:0000264	leucyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	185784	SO:0000265	SO:0000265	lysyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	185785	SO:0000266	SO:0000266	methionyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	185786	SO:0000267	SO:0000267	phenylalanyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	185787	SO:0000268	SO:0000268	prolyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	185788	SO:0000269	SO:0000269	seryl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	185789	SO:0000270	SO:0000270	threonyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	185790	SO:0000271	SO:0000271	tryptophanyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	185791	SO:0000272	SO:0000272	tyrosyl_tRNA	SO:0000253
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	185792	SO:0000273	SO:0000273	valyl_tRNA	SO:0000253
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SO	185793	SO:0000274	SO:0000274	snRNA	SO:0000655
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SO	185794	SO:0000275	SO:0000275	snoRNA	SO:0000655
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SOFA	small_regulatory_ncRNA	SOFA	SOFA	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	185795	SO:0000276	SO:0000276	miRNA	SO:0000370
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that is bound by another molecule." [SO:ke]	SO	185796	SO:0000277	SO:0000277	bound_by_factor	SO:0000733
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is bound by a nucleic acid." [SO:xp]	SO	185797	SO:0000278	SO:0000278	transcript_bound_by_nucleic_acid	SO:0000673
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is bound by a protein." [SO:xp]	SO	185798	SO:0000279	SO:0000279	transcript_bound_by_protein	SO:0000673
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is engineered." [SO:xp]	SO	185799	SO:0000280	SO:0000280	engineered_gene	SO:0000704
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A gene that is engineered." [SO:xp]	SO	185800	SO:0000280	SO:0000280	engineered_gene	SO:0000804
1	"A gene that is engineered." [SO:xp]	\N	engineered_gene	\N	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	185801	SO:0000281	SO:0000281	engineered_foreign_gene	SO:0000280
1	"A gene that is foreign." [SO:xp]	\N	foreign_gene	\N	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	185802	SO:0000281	SO:0000281	engineered_foreign_gene	SO:0000285
1	"A region that is engineered and foreign." [SO:xp]	\N	engineered_foreign_region	\N	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	185803	SO:0000281	SO:0000281	engineered_foreign_gene	SO:0000805
1	"An mRNA with a frameshift." [SO:xp]	\N	mRNA_with_frameshift	\N	\N	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	185804	SO:0000282	SO:0000282	mRNA_with_minus_1_frameshift	SO:0000108
1	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	\N	transposable_element_gene	\N	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	185805	SO:0000283	SO:0000283	engineered_foreign_transposable_element_gene	SO:0000111
1	"A gene that is engineered and foreign." [SO:xp]	\N	engineered_foreign_gene	\N	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	185806	SO:0000283	SO:0000283	engineered_foreign_transposable_element_gene	SO:0000281
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is foreign." [SO:xp]	SO	185807	SO:0000285	SO:0000285	foreign_gene	SO:0000704
1	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185808	SO:0000286	SO:0000286	long_terminal_repeat	SO:0000657
1	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185809	SO:0000286	SO:0000286	long_terminal_repeat	SO:0000186
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is a fusion." [SO:xp]	SO	185810	SO:0000287	SO:0000287	fusion_gene	SO:0000704
1	"A gene that is engineered." [SO:xp]	\N	engineered_gene	\N	\N	sequence	"A fusion gene that is engineered." [SO:xp]	SO	185811	SO:0000288	SO:0000288	engineered_fusion_gene	SO:0000280
1	"A gene that is a fusion." [SO:xp]	\N	fusion_gene	\N	\N	sequence	"A fusion gene that is engineered." [SO:xp]	SO	185812	SO:0000288	SO:0000288	engineered_fusion_gene	SO:0000287
1	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	satellite_DNA	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	SO	185813	SO:0000289	SO:0000289	microsatellite	SO:0000005
1	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	\N	microsatellite	SOFA	\N	sequence	"" []	SO	185814	SO:0000290	SO:0000290	dinucleotide_repeat_microsatellite_feature	SO:0000289
1	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	\N	microsatellite	SOFA	\N	sequence	"" []	SO	185815	SO:0000291	SO:0000291	trinucleotide_repeat_microsatellite_feature	SO:0000289
1	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	185816	SO:0000293	SO:0000293	engineered_foreign_repetitive_element	SO:0000657
1	"A region that is engineered and foreign." [SO:xp]	\N	engineered_foreign_region	\N	\N	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	185817	SO:0000293	SO:0000293	engineered_foreign_repetitive_element	SO:0000805
1	"A region of sequence containing one or more repeat units." [SO:ke]	SOFA	repeat_region	SOFA	SOFA	sequence	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	SO	185818	SO:0000294	SO:0000294	inverted_repeat	SO:0000657
1	"An intron which is spliced by the spliceosome." [SO:ke]	\N	spliceosomal_intron	SOFA	\N	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	185819	SO:0000295	SO:0000295	U12_intron	SO:0000662
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185820	SO:0000296	SO:0000296	origin_of_replication	SO:0001411
1	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185821	SO:0000296	SO:0000296	origin_of_replication	SO:0001235
1	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	origin_of_replication	SOFA	\N	sequence	"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185822	SO:0000297	SO:0000297	D_loop	SO:0000296
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	185823	SO:0000298	SO:0000298	recombination_feature	SO:0001411
1	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	185824	SO:0000299	SO:0000299	specific_recombination_site	SO:0000669
1	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	185825	SO:0000300	SO:0000300	recombination_feature_of_rearranged_gene	SO:0000299
1	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	185826	SO:0000301	SO:0000301	vertebrate_immune_system_gene_recombination_feature	SO:0000300
1	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	185827	SO:0000302	SO:0000302	J_gene_recombination_feature	SO:0000939
1	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	185828	SO:0000303	SO:0000303	clip	SO:0000835
1	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SOFA	base	SOFA	SOFA	sequence	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185829	SO:0000305	SO:0000305	modified_DNA_base	SO:0001236
1	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SOFA	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185830	SO:0000305	SO:0000305	modified_DNA_base	SO:0001720
1	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	modified_DNA_base	SOFA	SOFA	sequence	"A nucleotide modified by methylation." [SO:ke]	SO	185831	SO:0000306	SO:0000306	methylated_DNA_base_feature	SO:0000305
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]	SO	185832	SO:0000307	SO:0000307	CpG_island	SO:0001411
1	"An attribute to describe a feature that has been proven." [SO:ke]	\N	validated	\N	\N	sequence	"Attribute to describe a feature that has been experimentally verified." [SO:ke]	SO	185833	SO:0000312	SO:0000312	experimentally_determined	SO:0000789
1	"A folded RNA sequence." [SO:ke]	\N	RNA_sequence_secondary_structure	\N	\N	sequence	"A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185834	SO:0000313	SO:0000313	stem_loop	SO:0000122
1	"A region of sequence containing one or more repeat units." [SO:ke]	SOFA	repeat_region	SOFA	SOFA	sequence	"A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]	SO	185835	SO:0000314	SO:0000314	direct_repeat	SO:0000657
1	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	185836	SO:0000315	SO:0000315	TSS	SO:0000835
1	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	185837	SO:0000316	SO:0000316	CDS	SO:0000836
1	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	185838	SO:0000317	SO:0000317	cDNA_clone	SO:0000151
1	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SOFA	codon	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	185839	SO:0000318	SO:0000318	start_codon	SO:0000360
1	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SOFA	codon	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	185840	SO:0000319	SO:0000319	stop_codon	SO:0000360
1	"Region of a transcript that regulates splicing." [SO:ke]	\N	splice_enhancer	SOFA	\N	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	185841	SO:0000320	SO:0000320	intronic_splice_enhancer	SO:0000344
1	"A region within an intron." [SO:ke]	\N	spliceosomal_intron_region	SOFA	\N	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	185842	SO:0000320	SO:0000320	intronic_splice_enhancer	SO:0000841
1	"An mRNA with a frameshift." [SO:xp]	\N	mRNA_with_frameshift	\N	\N	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	185843	SO:0000321	SO:0000321	mRNA_with_plus_1_frameshift	SO:0000108
1	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	\N	nuclease_sensitive_site	SOFA	\N	sequence	"" []	SO	185844	SO:0000322	SO:0000322	nuclease_hypersensitive_site	SO:0000684
1	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	\N	sequence	"The first base to be translated into protein." [SO:ke]	SO	185845	SO:0000323	SO:0000323	coding_start	SO:0000851
1	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	SOFA	sequence	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SO	185846	SO:0000324	SO:0000324	tag	SO:0000696
1	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SOFA	rRNA_primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	185847	SO:0000325	SO:0000325	rRNA_large_subunit_primary_transcript	SO:0000209
1	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SOFA	tag	SOFA	SOFA	sequence	"A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	SO	185848	SO:0000326	SO:0000326	SAGE_tag	SO:0000324
1	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	\N	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	185849	SO:0000327	SO:0000327	coding_end	SO:0000851
1	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	\N	probe	\N	\N	sequence	"" []	SO	185850	SO:0000328	SO:0000328	microarray_oligo	SO:0000051
1	"An mRNA with a frameshift." [SO:xp]	\N	mRNA_with_frameshift	\N	\N	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	185851	SO:0000329	SO:0000329	mRNA_with_plus_2_frameshift	SO:0000108
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	185852	SO:0000330	SO:0000330	conserved_region	SO:0001410
1	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SOFA	tag	SOFA	SOFA	sequence	"Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]	SO	185853	SO:0000331	SO:0000331	STS	SO:0000324
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	SOFA	conserved_region	SOFA	SOFA	sequence	"Coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	185854	SO:0000332	SO:0000332	coding_conserved_region	SO:0000330
1	"A sequence_feature with an extent of zero." [SO:ke]	SOFA	junction	SOFA	SOFA	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	185855	SO:0000333	SO:0000333	exon_junction	SO:0000699
1	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	185856	SO:0000333	SO:0000333	exon_junction	SO:0000233
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	SOFA	conserved_region	SOFA	SOFA	sequence	"Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	185857	SO:0000334	SO:0000334	nc_conserved_region	SO:0000330
1	"An mRNA with a frameshift." [SO:xp]	\N	mRNA_with_frameshift	\N	\N	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	185858	SO:0000335	SO:0000335	mRNA_with_minus_2_frameshift	SO:0000108
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	185859	SO:0000336	SO:0000336	pseudogene	SO:0001411
1	"A double stranded oligonucleotide." [SO:ke]	SOFA	ds_oligo	SOFA	SOFA	sequence	"A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]	SO	185860	SO:0000337	SO:0000337	RNAi_reagent	SO:0000442
1	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	\N	terminal_inverted_repeat_element	\N	\N	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	185861	SO:0000338	SO:0000338	MITE	SO:0000208
1	"" []	\N	recombination_feature	\N	\N	sequence	"A region in a genome which promotes recombination." [SO:rd]	SO	185862	SO:0000339	SO:0000339	recombination_hotspot	SO:0000298
1	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SO	185863	SO:0000340	SO:0000340	chromosome	SO:0001235
1	"A region of a chromosome." [SO:ke]	SOFA	chromosome_part	SOFA	SOFA	sequence	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SO	185864	SO:0000341	SO:0000341	chromosome_band	SO:0000830
1	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	185865	SO:0000342	SO:0000342	site_specific_recombination_target_region	SO:0000299
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SO	185866	SO:0000343	SO:0000343	match	SO:0001410
1	"A regulatory_region that modulates splicing." [SO:ke]	SOFA	splicing_regulatory_region	SOFA	SOFA	sequence	"Region of a transcript that regulates splicing." [SO:ke]	SO	185867	SO:0000344	SO:0000344	splice_enhancer	SO:0001056
1	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SOFA	tag	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	SO	185868	SO:0000345	SO:0000345	EST	SO:0000324
1	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	\N	resolution_site	\N	\N	sequence	"" []	SO	185869	SO:0000346	SO:0000346	loxP_site	SO:0000947
1	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	SOFA	sequence	"A match against a nucleotide sequence." [SO:ke]	SO	185870	SO:0000347	SO:0000347	nucleotide_match	SO:0000343
1	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	SO	185871	SO:0000348	SO:0000348	nucleic_acid	SO:0000443
1	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	SOFA	sequence	"A match against a protein sequence." [SO:ke]	SO	185872	SO:0000349	SO:0000349	protein_match	SO:0000343
1	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	\N	inversion_site	\N	\N	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	185873	SO:0000350	SO:0000350	FRT_site	SO:0000948
1	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]	SO	185874	SO:0000351	SO:0000351	synthetic_sequence	SO:0000443
1	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	SO	185875	SO:0000352	SO:0000352	DNA	SO:0000348
1	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SO	185876	SO:0000353	SO:0000353	sequence_assembly	SO:0001248
1	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	\N	nuclease_sensitive_site	SOFA	\N	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	185877	SO:0000354	SO:0000354	group_1_intron_homing_endonuclease_target_region	SO:0000684
1	"" []	\N	recombination_feature	\N	\N	sequence	"A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]	SO	185878	SO:0000355	SO:0000355	haplotype_block	SO:0000298
1	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb]	SO	185879	SO:0000356	SO:0000356	RNA	SO:0000348
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]	SO	185880	SO:0000357	SO:0000357	flanked	SO:0000733
1	"An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]	\N	flanked	\N	\N	sequence	"An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]	SO	185881	SO:0000359	SO:0000359	floxed	SO:0000357
1	"A region of a CDS." [SO:cb]	SOFA	CDS_region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	185882	SO:0000360	SO:0000360	codon	SO:0000851
1	"An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]	\N	flanked	\N	\N	sequence	"An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]	SO	185883	SO:0000361	SO:0000361	FRT_flanked	SO:0000357
1	"An attribute describing a feature that is invalidated." [SO:ke]	\N	invalidated	\N	\N	sequence	"A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]	SO	185884	SO:0000362	SO:0000362	invalidated_by_chimeric_cDNA	SO:0000790
1	"A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]	\N	transgene	\N	\N	sequence	"A transgene that is floxed." [SO:xp]	SO	185885	SO:0000363	SO:0000363	floxed_gene	SO:0000902
1	"The sequences extending on either side of a specific region." [SO:ke]	\N	flanking_region	SOFA	\N	sequence	"The region of sequence surrounding a transposable element." [SO:ke]	SO	185886	SO:0000364	SO:0000364	transposable_element_flanking_region	SO:0000239
1	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	SO	185887	SO:0000365	SO:0000365	integron	SO:0001039
1	"A sequence_feature with an extent of zero." [SO:ke]	SOFA	junction	SOFA	SOFA	sequence	"The junction where an insertion occurred." [SO:ke]	SO	185888	SO:0000366	SO:0000366	insertion_site	SO:0000699
1	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	\N	integration_excision_site	\N	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	185889	SO:0000367	SO:0000367	attI_site	SO:0000946
1	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	\N	integron	\N	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	185890	SO:0000367	SO:0000367	attI_site	SO:0000365
1	"The junction where an insertion occurred." [SO:ke]	SOFA	insertion_site	SOFA	SOFA	sequence	"The junction in a genome where a transposable_element has inserted." [SO:ke]	SO	185891	SO:0000368	SO:0000368	transposable_element_insertion_site	SO:0000366
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SO	185892	SO:0000370	SO:0000370	small_regulatory_ncRNA	SO:0000655
1	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	185893	SO:0000371	SO:0000371	conjugative_transposon	SO:0000182
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	185894	SO:0000372	SO:0000372	enzymatic_RNA	SO:0000673
1	"A gene that is recombinationally rearranged." [SO:ke]	\N	recombinationally_rearranged_gene	\N	\N	sequence	"A recombinationally rearranged gene by inversion." [SO:xp]	SO	185895	SO:0000373	SO:0000373	recombinationally_inverted_gene	SO:0000456
1	"An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SOFA	enzymatic_RNA	SOFA	SOFA	sequence	"An RNA with catalytic activity." [SO:ma]	SO	185896	SO:0000374	SO:0000374	ribozyme	SO:0000372
1	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SOFA	large_subunit_rRNA	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	185897	SO:0000375	SO:0000375	rRNA_5_8S	SO:0000651
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	185898	SO:0000376	SO:0000376	RNA_6S	SO:0000370
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	185899	SO:0000377	SO:0000377	CsrB_RsmB_RNA	SO:0000370
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	185900	SO:0000378	SO:0000378	DsrA_RNA	SO:0000370
1	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	\N	DsrA_RNA	\N	\N	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	185901	SO:0000379	SO:0000379	GcvB_RNA	SO:0000378
1	"A motif that is active in RNA sequence." [SO:ke]	SOFA	RNA_motif	SOFA	SOFA	sequence	"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]	SO	185902	SO:0000380	SO:0000380	hammerhead_ribozyme	SO:0000715
1	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	\N	group_II_intron	SOFA	\N	sequence	"" []	SO	185903	SO:0000381	SO:0000381	group_IIA_intron	SO:0000603
1	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	\N	group_II_intron	SOFA	\N	sequence	"" []	SO	185904	SO:0000382	SO:0000382	group_IIB_intron	SO:0000603
1	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	\N	antisense_RNA	SOFA	\N	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	185905	SO:0000383	SO:0000383	MicF_RNA	SO:0000644
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	185906	SO:0000384	SO:0000384	OxyS_RNA	SO:0000370
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SO	185907	SO:0000385	SO:0000385	RNase_MRP_RNA	SO:0000655
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SO	185908	SO:0000386	SO:0000386	RNase_P_RNA	SO:0000655
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	185909	SO:0000387	SO:0000387	RprA_RNA	SO:0000370
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	185910	SO:0000388	SO:0000388	RRE_RNA	SO:0000370
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	185911	SO:0000389	SO:0000389	spot_42_RNA	SO:0000370
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SO	185912	SO:0000390	SO:0000390	telomerase_RNA	SO:0000655
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	185913	SO:0000391	SO:0000391	U1_snRNA	SO:0000274
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	185914	SO:0000392	SO:0000392	U2_snRNA	SO:0000274
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	185915	SO:0000393	SO:0000393	U4_snRNA	SO:0000274
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	185916	SO:0000394	SO:0000394	U4atac_snRNA	SO:0000274
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	185917	SO:0000395	SO:0000395	U5_snRNA	SO:0000274
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	185918	SO:0000396	SO:0000396	U6_snRNA	SO:0000274
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	185919	SO:0000397	SO:0000397	U6atac_snRNA	SO:0000274
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	185920	SO:0000398	SO:0000398	U11_snRNA	SO:0000274
1	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SOFA	snRNA	SOFA	SOFA	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	185921	SO:0000399	SO:0000399	U12_snRNA	SO:0000274
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	185922	SO:0000401	SO:0000401	gene_attribute	SO:0000733
1	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SOFA	C_D_box_snoRNA	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	185923	SO:0000403	SO:0000403	U14_snoRNA	SO:0000593
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SO	185924	SO:0000404	SO:0000404	vault_RNA	SO:0000655
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SO	185925	SO:0000405	SO:0000405	Y_RNA	SO:0000655
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	185926	SO:0000406	SO:0000406	twintron	SO:0000188
1	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SOFA	small_subunit_rRNA	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	185927	SO:0000407	SO:0000407	rRNA_18S	SO:0000650
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SO	185928	SO:0000409	SO:0000409	binding_site	SO:0001411
1	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SOFA	binding_site	biosapiens,SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SO	185929	SO:0000410	SO:0000410	protein_binding_site	SO:0000409
1	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	\N	sequence	"A region that rescues." [SO:xp]	SO	185930	SO:0000411	SO:0000411	rescue_region	SO:0000695
1	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]	SO	185931	SO:0000412	SO:0000412	restriction_fragment	SO:0000143
1	"A comment about the sequence." [SO:ke]	SOFA	remark	SOFA	SOFA	sequence	"A region where the sequence differs from that of a specified sequence." [SO:ke]	SO	185932	SO:0000413	SO:0000413	sequence_difference	SO:0000700
1	"An attribute describing a feature that is invalidated." [SO:ke]	\N	invalidated	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]	SO	185933	SO:0000414	SO:0000414	invalidated_by_genomic_contamination	SO:0000790
1	"An attribute describing a feature that is invalidated." [SO:ke]	\N	invalidated	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]	SO	185934	SO:0000415	SO:0000415	invalidated_by_genomic_polyA_primed_cDNA	SO:0000790
1	"An attribute describing a feature that is invalidated." [SO:ke]	\N	invalidated	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]	SO	185935	SO:0000416	SO:0000416	invalidated_by_partial_processing	SO:0000790
1	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	185936	SO:0000417	SO:0000417	polypeptide_domain	SO:0001070
1	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	185937	SO:0000417	SO:0000417	polypeptide_domain	SO:0100021
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	biosapiens,SOFA	peptide_localization_signal	SOFA	biosapiens,SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185938	SO:0000418	SO:0000418	signal_peptide	SO:0001527
1	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	biosapiens,SOFA	propeptide	biosapiens	biosapiens,SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	185939	SO:0000418	SO:0000418	signal_peptide	SO:0001062
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	185940	SO:0000419	SO:0000419	mature_protein_region	SO:0000839
1	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens,SOFA	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	185941	SO:0000419	SO:0000419	mature_protein_region	SO:0001063
1	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	\N	terminal_inverted_repeat	\N	\N	sequence	"" []	SO	185942	SO:0000420	SO:0000420	five_prime_terminal_inverted_repeat	SO:0000481
1	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	\N	terminal_inverted_repeat	\N	\N	sequence	"" []	SO	185943	SO:0000421	SO:0000421	three_prime_terminal_inverted_repeat	SO:0000481
1	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	185944	SO:0000422	SO:0000422	U5_LTR_region	SO:0000848
1	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	185945	SO:0000423	SO:0000423	R_LTR_region	SO:0000848
1	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	185946	SO:0000424	SO:0000424	U3_LTR_region	SO:0000848
1	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	185947	SO:0000425	SO:0000425	five_prime_LTR	SO:0000286
1	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	185948	SO:0000426	SO:0000426	three_prime_LTR	SO:0000286
1	"" []	\N	R_LTR_region	\N	\N	sequence	"" []	SO	185949	SO:0000427	SO:0000427	R_five_prime_LTR_region	SO:0000423
1	"" []	\N	five_prime_LTR_component	\N	\N	sequence	"" []	SO	185950	SO:0000427	SO:0000427	R_five_prime_LTR_region	SO:0000850
1	"" []	\N	U5_LTR_region	\N	\N	sequence	"" []	SO	185951	SO:0000428	SO:0000428	U5_five_prime_LTR_region	SO:0000422
1	"" []	\N	five_prime_LTR_component	\N	\N	sequence	"" []	SO	185952	SO:0000428	SO:0000428	U5_five_prime_LTR_region	SO:0000850
1	"" []	\N	U3_LTR_region	\N	\N	sequence	"" []	SO	185953	SO:0000429	SO:0000429	U3_five_prime_LTR_region	SO:0000424
1	"" []	\N	five_prime_LTR_component	\N	\N	sequence	"" []	SO	185954	SO:0000429	SO:0000429	U3_five_prime_LTR_region	SO:0000850
1	"" []	\N	three_prime_LTR_component	\N	\N	sequence	"" []	SO	185955	SO:0000430	SO:0000430	R_three_prime_LTR_region	SO:0000849
1	"" []	\N	three_prime_LTR_component	\N	\N	sequence	"" []	SO	185956	SO:0000431	SO:0000431	U3_three_prime_LTR_region	SO:0000849
1	"" []	\N	three_prime_LTR_component	\N	\N	sequence	"" []	SO	185957	SO:0000432	SO:0000432	U5_three_prime_LTR_region	SO:0000849
1	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	185958	SO:0000433	SO:0000433	non_LTR_retrotransposon_polymeric_tract	SO:0000657
1	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	185959	SO:0000433	SO:0000433	non_LTR_retrotransposon_polymeric_tract	SO:0000840
1	"A retrotransposon without long terminal repeat sequences." [SO:ke]	\N	non_LTR_retrotransposon	\N	\N	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	185960	SO:0000433	SO:0000433	non_LTR_retrotransposon_polymeric_tract	SO:0000189
1	"A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]	\N	direct_repeat	SOFA	\N	sequence	"A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]	SO	185961	SO:0000434	SO:0000434	target_site_duplication	SO:0000314
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	185962	SO:0000435	SO:0000435	RR_tract	SO:0000330
1	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	185963	SO:0000435	SO:0000435	RR_tract	SO:0000186
1	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	origin_of_replication	SOFA	SOFA	sequence	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	SO	185964	SO:0000436	SO:0000436	ARS	SO:0000296
1	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	\N	chromosomal_inversion	\N	\N	sequence	"" []	SO	185965	SO:0000439	SO:0000439	inverted_ring_chromosome	SO:1000030
1	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	\N	ring_chromosome	\N	\N	sequence	"" []	SO	185966	SO:0000439	SO:0000439	inverted_ring_chromosome	SO:1000045
1	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	185967	SO:0000440	SO:0000440	vector_replicon	SO:0001235
1	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	185968	SO:0000440	SO:0000440	vector_replicon	SO:0000151
1	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	SOFA	sequence	"A single stranded oligonucleotide." [SO:ke]	SO	185969	SO:0000441	SO:0000441	ss_oligo	SO:0000696
1	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	SOFA	sequence	"A double stranded oligonucleotide." [SO:ke]	SO	185970	SO:0000442	SO:0000442	ds_oligo	SO:0000696
1	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe the kind of biological sequence." [SO:ke]	SO	185971	SO:0000443	SO:0000443	polymer_attribute	SO:0000400
1	"An exon that does not contain any codons." [SO:ke]	\N	noncoding_exon	SOFA	\N	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	185972	SO:0000444	SO:0000444	three_prime_noncoding_exon	SO:0000198
1	"An exon that does not contain any codons." [SO:ke]	\N	noncoding_exon	SOFA	\N	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	185973	SO:0000445	SO:0000445	five_prime_noncoding_exon	SO:0000198
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"Intron located in the untranslated region." [SO:ke]	SO	185974	SO:0000446	SO:0000446	UTR_intron	SO:0000188
1	"Intron located in the untranslated region." [SO:ke]	\N	UTR_intron	\N	\N	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	185975	SO:0000447	SO:0000447	five_prime_UTR_intron	SO:0000446
1	"Intron located in the untranslated region." [SO:ke]	\N	UTR_intron	\N	\N	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	185976	SO:0000448	SO:0000448	three_prime_UTR_intron	SO:0000446
1	"An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]	\N	synthetic_sequence	\N	\N	sequence	"A sequence of nucleotides or amino acids which, by design, has a \\"random\\" order of components, given a predetermined input frequency of these components." [SO:ma]	SO	185977	SO:0000449	SO:0000449	random_sequence	SO:0000351
1	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	\N	sequence	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	SO	185978	SO:0000450	SO:0000450	interband	SO:0000830
1	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene that encodes a polyadenylated mRNA." [SO:xp]	SO	185979	SO:0000451	SO:0000451	gene_with_polyadenylated_mRNA	SO:0001217
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	185980	SO:0000453	SO:0000453	chromosomal_transposition	SO:1000183
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SO	185981	SO:0000454	SO:0000454	rasiRNA	SO:0000655
1	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene that encodes an mRNA with a frameshift." [SO:xp]	SO	185982	SO:0000455	SO:0000455	gene_with_mRNA_with_frameshift	SO:0001217
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is recombinationally rearranged." [SO:ke]	SO	185983	SO:0000456	SO:0000456	recombinationally_rearranged_gene	SO:0000704
1	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	185984	SO:0000457	SO:0000457	interchromosomal_duplication	SO:1000037
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_segment	\N	\N	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	185985	SO:0000458	SO:0000458	D_gene_segment	SO:0000460
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene with a transcript that is trans-spliced." [SO:xp]	SO	185986	SO:0000459	SO:0000459	gene_with_trans_spliced_transcript	SO:0000704
1	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	185987	SO:0000460	SO:0000460	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000301
1	"An incomplete chromosome." [SO:ke]	\N	chromosomal_deletion	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	185988	SO:0000461	SO:0000461	inversion_derived_bipartite_deficiency	SO:1000029
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A non-functional descendant of a functional entity." [SO:cjm]	SO	185989	SO:0000462	SO:0000462	pseudogenic_region	SO:0001411
1	"" []	\N	gene_attribute	\N	\N	sequence	"A gene that encodes more than one transcript." [SO:ke]	SO	185990	SO:0000463	SO:0000463	encodes_alternately_spliced_transcripts	SO:0000401
1	"A non-functional descendant of a functional entity." [SO:cjm]	SOFA	pseudogenic_region	SOFA	SOFA	sequence	"A non-functional descendant of an exon." [SO:ke]	SO	185991	SO:0000464	SO:0000464	decayed_exon	SO:0000462
1	"An incomplete chromosome." [SO:ke]	\N	chromosomal_deletion	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	185992	SO:0000465	SO:0000465	inversion_derived_deficiency_plus_duplication	SO:1000029
1	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	185993	SO:0000465	SO:0000465	inversion_derived_deficiency_plus_duplication	SO:1000038
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_segment	\N	\N	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	185994	SO:0000466	SO:0000466	V_gene_segment	SO:0000460
1	"An attribute describing a gene that is regulated after it has been translated." [SO:ke]	\N	post_translationally_regulated	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]	SO	185995	SO:0000467	SO:0000467	post_translationally_regulated_by_protein_stability	SO:0000130
1	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	185996	SO:0000468	SO:0000468	golden_path_fragment	SO:0000143
1	"A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]	SOFA	golden_path	SOFA	SOFA	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	185997	SO:0000468	SO:0000468	golden_path_fragment	SO:0000688
1	"An attribute describing a gene that is regulated after it has been translated." [SO:ke]	\N	post_translationally_regulated	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]	SO	185998	SO:0000469	SO:0000469	post_translationally_regulated_by_protein_modification	SO:0000130
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_segment	\N	\N	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	185999	SO:0000470	SO:0000470	J_gene_segment	SO:0000460
1	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation." [SO:ke]	SO	186000	SO:0000471	SO:0000471	autoregulated	SO:0000123
1	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	SO	186001	SO:0000472	SO:0000472	tiling_path	SO:0000353
1	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	186002	SO:0000473	SO:0000473	negatively_autoregulated	SO:0000126
1	"The gene product is involved in its own transcriptional regulation." [SO:ke]	\N	autoregulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	186003	SO:0000473	SO:0000473	negatively_autoregulated	SO:0000471
1	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	186004	SO:0000474	SO:0000474	tiling_path_fragment	SO:0000143
1	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	SOFA	tiling_path	SOFA	SOFA	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	186005	SO:0000474	SO:0000474	tiling_path_fragment	SO:0000472
1	"An inducer molecule is required for transcription to occur." [SO:ke]	\N	transcriptionally_induced	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	186006	SO:0000475	SO:0000475	positively_autoregulated	SO:0000125
1	"The gene product is involved in its own transcriptional regulation." [SO:ke]	\N	autoregulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	186007	SO:0000475	SO:0000475	positively_autoregulated	SO:0000471
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	186008	SO:0000476	SO:0000476	contig_read	SO:0000150
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_segment	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186009	SO:0000478	SO:0000478	C_gene_segment	SO:0000460
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is trans-spliced." [SO:xp]	SO	186010	SO:0000479	SO:0000479	trans_spliced_transcript	SO:0000673
1	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	186011	SO:0000480	SO:0000480	tiling_path_clone	SO:0000151
1	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	\N	tiling_path_fragment	SOFA	\N	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	186012	SO:0000480	SO:0000480	tiling_path_clone	SO:0000474
1	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	\N	inverted_repeat	SOFA	\N	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	186013	SO:0000481	SO:0000481	terminal_inverted_repeat	SO:0000294
1	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	\N	terminal_inverted_repeat_element	\N	\N	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	186014	SO:0000481	SO:0000481	terminal_inverted_repeat	SO:0000208
1	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	186015	SO:0000482	SO:0000482	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000301
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A primary transcript that is never translated into a protein." [SO:ke]	SO	186016	SO:0000483	SO:0000483	nc_primary_transcript	SO:0000185
1	"The maximal intersection of exon and UTR." [SO:ke]	SOFA	noncoding_region_of_exon	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	186017	SO:0000484	SO:0000484	three_prime_coding_exon_noncoding_region	SO:0001214
1	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SOFA	three_prime_coding_exon	\N	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	186018	SO:0000484	SO:0000484	three_prime_coding_exon_noncoding_region	SO:0000202
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186019	SO:0000485	SO:0000485	DJ_J_cluster	SO:0000938
1	"The maximal intersection of exon and UTR." [SO:ke]	SOFA	noncoding_region_of_exon	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	186020	SO:0000486	SO:0000486	five_prime_coding_exon_noncoding_region	SO:0001214
1	"The 5' most coding exon." [SO:ke]	SOFA	five_prime_coding_exon	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	186021	SO:0000486	SO:0000486	five_prime_coding_exon_noncoding_region	SO:0000200
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186022	SO:0000487	SO:0000487	VDJ_J_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186023	SO:0000488	SO:0000488	VDJ_J_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186024	SO:0000489	SO:0000489	VJ_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186025	SO:0000490	SO:0000490	VJ_J_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186026	SO:0000491	SO:0000491	VJ_J_cluster	SO:0000938
1	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"" []	SO	186027	SO:0000492	SO:0000492	D_gene_recombination_feature	SO:0000939
1	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186028	SO:0000493	SO:0000493	three_prime_D_heptamer	SO:0000561
1	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	three_prime_D_recombination_signal_sequence	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186029	SO:0000493	SO:0000493	three_prime_D_heptamer	SO:0000570
1	"" []	\N	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186030	SO:0000494	SO:0000494	three_prime_D_nonamer	SO:0000562
1	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	three_prime_D_recombination_signal_sequence	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186031	SO:0000494	SO:0000494	three_prime_D_nonamer	SO:0000570
1	"" []	\N	vertebrate_immune_system_gene_recombination_spacer	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186032	SO:0000495	SO:0000495	three_prime_D_spacer	SO:0000563
1	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	three_prime_D_recombination_signal_sequence	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186033	SO:0000495	SO:0000495	three_prime_D_spacer	SO:0000570
1	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186034	SO:0000496	SO:0000496	five_prime_D_heptamer	SO:0000561
1	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	five_prime_D_recombination_signal_sequence	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186035	SO:0000496	SO:0000496	five_prime_D_heptamer	SO:0000556
1	"" []	\N	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186036	SO:0000497	SO:0000497	five_prime_D_nonamer	SO:0000562
1	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	five_prime_D_recombination_signal_sequence	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186037	SO:0000497	SO:0000497	five_prime_D_nonamer	SO:0000556
1	"" []	\N	vertebrate_immune_system_gene_recombination_spacer	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186038	SO:0000498	SO:0000498	five_prime_D_spacer	SO:0000563
1	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	five_prime_D_recombination_signal_sequence	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186039	SO:0000498	SO:0000498	five_prime_D_spacer	SO:0000556
1	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]	SO	186040	SO:0000499	SO:0000499	virtual_sequence	SO:0000353
1	"" []	\N	base_pair	\N	\N	sequence	"A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]	SO	186041	SO:0000500	SO:0000500	Hoogsteen_base_pair	SO:0000028
1	"" []	\N	base_pair	\N	\N	sequence	"A type of non-canonical base-pairing." [SO:ke]	SO	186042	SO:0000501	SO:0000501	reverse_Hoogsteen_base_pair	SO:0000028
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186043	SO:0000504	SO:0000504	D_DJ_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186044	SO:0000505	SO:0000505	D_DJ_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186045	SO:0000506	SO:0000506	D_DJ_J_C_cluster	SO:0000938
1	"A non-functional descendant of a functional entity." [SO:cjm]	\N	pseudogenic_region	SOFA	\N	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	186046	SO:0000507	SO:0000507	pseudogenic_exon	SO:0000462
1	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	\N	pseudogenic_transcript	\N	\N	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	186047	SO:0000507	SO:0000507	pseudogenic_exon	SO:0000516
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186048	SO:0000508	SO:0000508	D_DJ_J_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186049	SO:0000509	SO:0000509	D_J_C_cluster	SO:0000482
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186050	SO:0000510	SO:0000510	VD_gene_segment	SO:0000936
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186051	SO:0000511	SO:0000511	J_C_cluster	SO:0000482
1	"An incomplete chromosome." [SO:ke]	\N	chromosomal_deletion	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	186052	SO:0000512	SO:0000512	inversion_derived_deficiency_plus_aneuploid	SO:1000029
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186053	SO:0000513	SO:0000513	J_cluster	SO:0000482
1	"" []	\N	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186054	SO:0000514	SO:0000514	J_nonamer	SO:0000562
1	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_gene_recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186055	SO:0000514	SO:0000514	J_nonamer	SO:0000302
1	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186056	SO:0000515	SO:0000515	J_heptamer	SO:0000561
1	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_gene_recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186057	SO:0000515	SO:0000515	J_heptamer	SO:0000302
1	"A non-functional descendant of a functional entity." [SO:cjm]	\N	pseudogenic_region	SOFA	\N	sequence	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	SO	186058	SO:0000516	SO:0000516	pseudogenic_transcript	SO:0000462
1	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	SO	186059	SO:0000516	SO:0000516	pseudogenic_transcript	SO:0000336
1	"" []	\N	vertebrate_immune_system_gene_recombination_spacer	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186060	SO:0000517	SO:0000517	J_spacer	SO:0000563
1	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	J_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186061	SO:0000517	SO:0000517	J_spacer	SO:0000302
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186062	SO:0000518	SO:0000518	V_DJ_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186063	SO:0000519	SO:0000519	V_DJ_J_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186064	SO:0000520	SO:0000520	V_VDJ_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186065	SO:0000521	SO:0000521	V_VDJ_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186066	SO:0000522	SO:0000522	V_VDJ_J_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186067	SO:0000523	SO:0000523	V_VJ_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186068	SO:0000524	SO:0000524	V_VJ_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186069	SO:0000525	SO:0000525	V_VJ_J_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186070	SO:0000526	SO:0000526	V_cluster	SO:0000482
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186071	SO:0000527	SO:0000527	V_D_DJ_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186072	SO:0000528	SO:0000528	V_D_DJ_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186073	SO:0000529	SO:0000529	V_D_DJ_J_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186074	SO:0000530	SO:0000530	V_D_DJ_J_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186075	SO:0000531	SO:0000531	V_D_J_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186076	SO:0000532	SO:0000532	V_D_J_cluster	SO:0000938
1	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186077	SO:0000533	SO:0000533	V_heptamer	SO:0000561
1	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_gene_recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186078	SO:0000533	SO:0000533	V_heptamer	SO:0000538
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186079	SO:0000534	SO:0000534	V_J_cluster	SO:0000482
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186080	SO:0000535	SO:0000535	V_J_C_cluster	SO:0000482
1	"" []	\N	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186081	SO:0000536	SO:0000536	V_nonamer	SO:0000562
1	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_gene_recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186082	SO:0000536	SO:0000536	V_nonamer	SO:0000538
1	"" []	\N	vertebrate_immune_system_gene_recombination_spacer	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186083	SO:0000537	SO:0000537	V_spacer	SO:0000563
1	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	\N	V_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186084	SO:0000537	SO:0000537	V_spacer	SO:0000538
1	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186085	SO:0000538	SO:0000538	V_gene_recombination_feature	SO:0000939
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186086	SO:0000539	SO:0000539	DJ_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186087	SO:0000540	SO:0000540	DJ_J_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186088	SO:0000541	SO:0000541	VDJ_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186089	SO:0000542	SO:0000542	V_DJ_C_cluster	SO:0000938
1	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	186090	SO:0000544	SO:0000544	helitron	SO:0000182
1	"A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]	\N	pseudoknot	\N	\N	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	186091	SO:0000545	SO:0000545	recoding_pseudoknot	SO:0000591
1	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	186092	SO:0000545	SO:0000545	recoding_pseudoknot	SO:1001268
1	"An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]	\N	synthetic_sequence	\N	\N	sequence	"" []	SO	186093	SO:0000546	SO:0000546	designed_sequence	SO:0000351
1	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	186094	SO:0000547	SO:0000547	inversion_derived_bipartite_duplication	SO:1000038
1	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene that encodes a transcript that is edited." [SO:xp]	SO	186095	SO:0000548	SO:0000548	gene_with_edited_transcript	SO:0001217
1	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	186096	SO:0000549	SO:0000549	inversion_derived_duplication_plus_aneuploid	SO:1000038
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	186097	SO:0000550	SO:0000550	aneuploid_chromosome	SO:1000183
1	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	186098	SO:0000551	SO:0000551	polyA_signal_sequence	SO:0001679
1	"Region in mRNA where ribosome assembles." [SO:ke]	\N	ribosome_entry_site	SOFA	\N	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	186099	SO:0000552	SO:0000552	Shine_Dalgarno_sequence	SO:0000139
1	"A sequence_feature with an extent of zero." [SO:ke]	SOFA	junction	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	186100	SO:0000553	SO:0000553	polyA_site	SO:0000699
1	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	three_prime_UTR	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	186101	SO:0000553	SO:0000553	polyA_site	SO:0000205
1	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	186102	SO:0000553	SO:0000553	polyA_site	SO:0000233
1	"Part of the primary transcript that is clipped off during processing." [SO:ke]	\N	clip	SOFA	\N	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	186103	SO:0000555	SO:0000555	five_prime_clip	SO:0000303
1	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186104	SO:0000556	SO:0000556	five_prime_D_recombination_signal_sequence	SO:0000492
1	"Part of the primary transcript that is clipped off during processing." [SO:ke]	\N	clip	SOFA	\N	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	186105	SO:0000557	SO:0000557	three_prime_clip	SO:0000303
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186106	SO:0000558	SO:0000558	C_cluster	SO:0000482
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186107	SO:0000559	SO:0000559	D_cluster	SO:0000482
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186108	SO:0000560	SO:0000560	D_J_cluster	SO:0000482
1	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186109	SO:0000561	SO:0000561	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000939
1	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"" []	SO	186110	SO:0000562	SO:0000562	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000939
1	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	186111	SO:0000563	SO:0000563	vertebrate_immune_system_gene_recombination_spacer	SO:0000301
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186112	SO:0000564	SO:0000564	V_DJ_J_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186113	SO:0000565	SO:0000565	V_VDJ_J_C_cluster	SO:0000938
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186114	SO:0000566	SO:0000566	V_VJ_J_C_cluster	SO:0000938
1	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	\N	aneuploid_chromosome	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	186115	SO:0000567	SO:0000567	inversion_derived_aneuploid_chromosome	SO:0000550
1	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"" []	SO	186116	SO:0000568	SO:0000568	bidirectional_promoter	SO:0000167
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke]	SO	186117	SO:0000569	SO:0000569	retrotransposed	SO:0000733
1	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186118	SO:0000570	SO:0000570	three_prime_D_recombination_signal_sequence	SO:0000492
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186119	SO:0000571	SO:0000571	miRNA_encoding	SO:0000011
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186120	SO:0000572	SO:0000572	DJ_gene_segment	SO:0000936
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186121	SO:0000573	SO:0000573	rRNA_encoding	SO:0000011
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186122	SO:0000574	SO:0000574	VDJ_gene_segment	SO:0000936
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186123	SO:0000575	SO:0000575	scRNA_encoding	SO:0000011
1	"" []	\N	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	186124	SO:0000576	SO:0000576	VJ_gene_segment	SO:0000936
1	"" []	SOFA	chromosomal_structural_element	SOFA	SOFA	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	186125	SO:0000577	SO:0000577	centromere	SO:0000628
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186126	SO:0000578	SO:0000578	snoRNA_encoding	SO:0000011
1	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	\N	sequence	"A locatable feature on a transcript that is edited." [SO:ma]	SO	186127	SO:0000579	SO:0000579	edited_transcript_feature	SO:0000833
1	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	\N	snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	186128	SO:0000580	SO:0000580	methylation_guide_snoRNA_primary_transcript	SO:0000232
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	186129	SO:0000581	SO:0000581	cap	SO:0001411
1	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	\N	snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	186130	SO:0000582	SO:0000582	rRNA_cleavage_snoRNA_primary_transcript	SO:0000232
1	"A locatable feature on a transcript that is edited." [SO:ma]	\N	edited_transcript_feature	\N	\N	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	186131	SO:0000583	SO:0000583	pre_edited_region	SO:0000579
1	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	186132	SO:0000584	SO:0000584	tmRNA	SO:0000370
1	"" []	\N	snoRNA_encoding	\N	\N	sequence	"" []	SO	186133	SO:0000585	SO:0000585	C_D_box_snoRNA_encoding	SO:0000578
1	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	SO	186134	SO:0000586	SO:0000586	tmRNA_primary_transcript	SO:0000483
1	"A self spliced intron." [SO:ke]	SOFA	autocatalytically_spliced_intron	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	186135	SO:0000587	SO:0000587	group_I_intron	SO:0000588
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	intron	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	186136	SO:0000588	SO:0000588	autocatalytically_spliced_intron	SO:0000188
1	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	SO	186137	SO:0000589	SO:0000589	SRP_RNA_primary_transcript	SO:0000483
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SO	186138	SO:0000590	SO:0000590	SRP_RNA	SO:0000655
1	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]	SO	186139	SO:0000591	SO:0000591	pseudoknot	SO:0000002
1	"A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]	\N	pseudoknot	\N	\N	sequence	"A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]	SO	186140	SO:0000592	SO:0000592	H_pseudoknot	SO:0000591
1	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SOFA	snoRNA	SOFA	SOFA	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	186141	SO:0000593	SO:0000593	C_D_box_snoRNA	SO:0000275
1	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	\N	snoRNA	SOFA	\N	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	186142	SO:0000594	SO:0000594	H_ACA_box_snoRNA	SO:0000275
1	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	\N	snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	186143	SO:0000595	SO:0000595	C_D_box_snoRNA_primary_transcript	SO:0000232
1	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	\N	snoRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	186144	SO:0000596	SO:0000596	H_ACA_box_snoRNA_primary_transcript	SO:0000232
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SO	186145	SO:0000602	SO:0000602	guide_RNA	SO:0000655
1	"A self spliced intron." [SO:ke]	SOFA	autocatalytically_spliced_intron	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	186146	SO:0000603	SO:0000603	group_II_intron	SO:0000588
1	"A locatable feature on a transcript that is edited." [SO:ma]	\N	edited_transcript_feature	\N	\N	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	186147	SO:0000604	SO:0000604	editing_block	SO:0000579
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]	SO	186148	SO:0000605	SO:0000605	intergenic_region	SO:0001411
1	"A locatable feature on a transcript that is edited." [SO:ma]	\N	edited_transcript_feature	\N	\N	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	186149	SO:0000606	SO:0000606	editing_domain	SO:0000579
1	"A locatable feature on a transcript that is edited." [SO:ma]	\N	edited_transcript_feature	\N	\N	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	186150	SO:0000607	SO:0000607	unedited_region	SO:0000579
1	"" []	\N	snoRNA_encoding	\N	\N	sequence	"" []	SO	186151	SO:0000608	SO:0000608	H_ACA_box_snoRNA_encoding	SO:0000578
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]	SO	186152	SO:0000609	SO:0000609	oligo_U_tail	SO:0001411
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]	SO	186153	SO:0000610	SO:0000610	polyA_sequence	SO:0001411
1	"A region within an intron." [SO:ke]	SOFA	spliceosomal_intron_region	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	186154	SO:0000611	SO:0000611	branch_site	SO:0000841
1	"A region within an intron." [SO:ke]	SOFA	spliceosomal_intron_region	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	186155	SO:0000612	SO:0000612	polypyrimidine_tract	SO:0000841
1	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	186156	SO:0000613	SO:0000613	bacterial_RNApol_promoter	SO:0000752
1	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	186157	SO:0000613	SO:0000613	bacterial_RNApol_promoter	SO:0001203
1	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	terminator	SOFA	\N	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	186158	SO:0000614	SO:0000614	bacterial_terminator	SO:0000141
1	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	186159	SO:0000614	SO:0000614	bacterial_terminator	SO:0000752
1	"" []	\N	eukaryotic_terminator	\N	\N	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	186160	SO:0000615	SO:0000615	terminator_of_type_2_RNApol_III_promoter	SO:0000951
1	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	186161	SO:0000616	SO:0000616	transcription_end_site	SO:0000835
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"" []	SO	186162	SO:0000617	SO:0000617	RNApol_III_promoter_type_1	SO:0000171
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"" []	SO	186163	SO:0000618	SO:0000618	RNApol_III_promoter_type_2	SO:0000171
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	186164	SO:0000619	SO:0000619	A_box	SO:0001660
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	186165	SO:0000620	SO:0000620	B_box	SO:0001660
1	"" []	\N	RNApol_III_promoter_type_2	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	186166	SO:0000620	SO:0000620	B_box	SO:0000618
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"" []	SO	186167	SO:0000621	SO:0000621	RNApol_III_promoter_type_3	SO:0000171
1	"" []	\N	core_promoter_element	\N	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	186168	SO:0000622	SO:0000622	C_box	SO:0001660
1	"" []	\N	RNApol_III_promoter_type_1	\N	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	186169	SO:0000622	SO:0000622	C_box	SO:0000617
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186170	SO:0000623	SO:0000623	snRNA_encoding	SO:0000011
1	"" []	SOFA	chromosomal_structural_element	SOFA	SOFA	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	186171	SO:0000624	SO:0000624	telomere	SO:0000628
1	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SOFA	CRM	SOFA	SOFA	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	186172	SO:0000625	SO:0000625	silencer	SO:0000727
1	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	\N	sequence	"" []	SO	186173	SO:0000626	SO:0000626	chromosomal_regulatory_element	SO:0000830
1	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SOFA	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SO	186174	SO:0000627	SO:0000627	insulator	SO:0001055
1	"A region of a chromosome." [SO:ke]	SOFA	chromosome_part	SOFA	SOFA	sequence	"" []	SO	186175	SO:0000628	SO:0000628	chromosomal_structural_element	SO:0000830
1	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"" []	SO	186176	SO:0000629	SO:0000629	five_prime_open_reading_frame	SO:0000836
1	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	five_prime_UTR	SOFA	\N	sequence	"" []	SO	186177	SO:0000629	SO:0000629	five_prime_open_reading_frame	SO:0000204
1	"A region of UTR." [SO:ke]	\N	UTR_region	SOFA	\N	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	186178	SO:0000630	SO:0000630	upstream_AUG_codon	SO:0000837
1	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	\N	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	186179	SO:0000630	SO:0000630	upstream_AUG_codon	SO:0000203
1	"A transcript that is polycistronic." [SO:xp]	\N	polycistronic_transcript	\N	\N	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	186180	SO:0000631	SO:0000631	polycistronic_primary_transcript	SO:0000078
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	186181	SO:0000631	SO:0000631	polycistronic_primary_transcript	SO:0000185
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	186182	SO:0000632	SO:0000632	monocistronic_primary_transcript	SO:0000185
1	"A transcript that is monocistronic." [SO:xp]	\N	monocistronic_transcript	\N	\N	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	186183	SO:0000632	SO:0000632	monocistronic_primary_transcript	SO:0000665
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	186184	SO:0000633	SO:0000633	monocistronic_mRNA	SO:0000234
1	"A transcript that is monocistronic." [SO:xp]	\N	monocistronic_transcript	\N	\N	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	186185	SO:0000633	SO:0000633	monocistronic_mRNA	SO:0000665
1	"A transcript that is polycistronic." [SO:xp]	\N	polycistronic_transcript	\N	\N	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	186186	SO:0000634	SO:0000634	polycistronic_mRNA	SO:0000078
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	186187	SO:0000634	SO:0000634	polycistronic_mRNA	SO:0000234
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	SO	186188	SO:0000635	SO:0000635	mini_exon_donor_RNA	SO:0000185
1	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"" []	SO	186189	SO:0000636	SO:0000636	spliced_leader_RNA	SO:0000835
1	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	\N	mini_exon_donor_RNA	\N	\N	sequence	"" []	SO	186190	SO:0000636	SO:0000636	spliced_leader_RNA	SO:0000635
1	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"A plasmid that is engineered." [SO:xp]	SO	186191	SO:0000637	SO:0000637	engineered_plasmid	SO:0000155
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A plasmid that is engineered." [SO:xp]	SO	186192	SO:0000637	SO:0000637	engineered_plasmid	SO:0000804
1	"A region of an rRNA primary transcript." [SO:ke]	\N	rRNA_primary_transcript_region	\N	\N	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	186193	SO:0000638	SO:0000638	transcribed_spacer_region	SO:0000838
1	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	\N	transcribed_spacer_region	\N	\N	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	186194	SO:0000639	SO:0000639	internal_transcribed_spacer_region	SO:0000638
1	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	\N	transcribed_spacer_region	\N	\N	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	186195	SO:0000640	SO:0000640	external_transcribed_spacer_region	SO:0000638
1	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	\N	microsatellite	SOFA	\N	sequence	"" []	SO	186196	SO:0000641	SO:0000641	tetranucleotide_repeat_microsatellite_feature	SO:0000289
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186197	SO:0000642	SO:0000642	SRP_RNA_encoding	SO:0000011
1	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	satellite_DNA	SOFA	SOFA	sequence	"A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]	SO	186198	SO:0000643	SO:0000643	minisatellite	SO:0000005
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SO	186199	SO:0000644	SO:0000644	antisense_RNA	SO:0000655
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"The reverse complement of the primary transcript." [SO:ke]	SO	186200	SO:0000645	SO:0000645	antisense_primary_transcript	SO:0000185
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SO	186201	SO:0000646	SO:0000646	siRNA	SO:0000655
1	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a micro RNA." [SO:ke]	SO	186202	SO:0000647	SO:0000647	miRNA_primary_transcript	SO:0000483
1	"A primary transcript encoding a micro RNA." [SO:ke]	\N	miRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	186203	SO:0000648	SO:0000648	stRNA_primary_transcript	SO:0000647
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SO	186204	SO:0000649	SO:0000649	stRNA	SO:0000655
1	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	186205	SO:0000650	SO:0000650	small_subunit_rRNA	SO:0000252
1	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	186206	SO:0000651	SO:0000651	large_subunit_rRNA	SO:0000252
1	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SOFA	large_subunit_rRNA	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	186207	SO:0000652	SO:0000652	rRNA_5S	SO:0000651
1	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SOFA	large_subunit_rRNA	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	186208	SO:0000653	SO:0000653	rRNA_28S	SO:0000651
1	"A gene located in kinetoplast sequence." [SO:xp]	\N	kinetoplast_gene	\N	\N	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	186209	SO:0000654	SO:0000654	maxicircle_gene	SO:0000089
1	"A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]	\N	maxicircle	\N	\N	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	186210	SO:0000654	SO:0000654	maxicircle_gene	SO:0000742
1	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SO	186211	SO:0000655	SO:0000655	ncRNA	SO:0000233
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186212	SO:0000656	SO:0000656	stRNA_encoding	SO:0000011
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of sequence containing one or more repeat units." [SO:ke]	SO	186213	SO:0000657	SO:0000657	repeat_region	SO:0001411
1	"A region of sequence containing one or more repeat units." [SO:ke]	SOFA	repeat_region	SOFA	SOFA	sequence	"A repeat that is located at dispersed sites in the genome." [SO:ke]	SO	186214	SO:0000658	SO:0000658	dispersed_repeat	SO:0000657
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186215	SO:0000659	SO:0000659	tmRNA_encoding	SO:0000011
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	intron	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	186216	SO:0000662	SO:0000662	spliceosomal_intron	SO:0000188
1	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	186217	SO:0000663	SO:0000663	tRNA_encoding	SO:0000011
1	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	\N	sequence	"" []	SO	186218	SO:0000664	SO:0000664	introgressed_chromosome_region	SO:0000830
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is monocistronic." [SO:xp]	SO	186219	SO:0000665	SO:0000665	monocistronic_transcript	SO:0000673
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	186220	SO:0000666	SO:0000666	mobile_intron	SO:0000188
1	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	186221	SO:0000666	SO:0000666	mobile_intron	SO:0001037
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR,SOFA	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	SO	186222	SO:0000667	SO:0000667	insertion	SO:0001059
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	DBVAR,SOFA	biological_region	SOFA	DBVAR,SOFA	sequence	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	SO	186223	SO:0000667	SO:0000667	insertion	SO:0001411
1	"A match to an EST or cDNA sequence." [SO:ke]	SOFA	expressed_sequence_match	SOFA	SOFA	sequence	"A match against an EST sequence." [SO:ke]	SO	186224	SO:0000668	SO:0000668	EST_match	SO:0000102
1	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	186225	SO:0000669	SO:0000669	sequence_rearrangement_feature	SO:0000298
1	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]	SO	186226	SO:0000670	SO:0000670	chromosome_breakage_sequence	SO:0000669
1	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]	SO	186227	SO:0000671	SO:0000671	internal_eliminated_sequence	SO:0000669
1	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]	SO	186228	SO:0000672	SO:0000672	macronucleus_destined_segment	SO:0000669
1	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SO	186229	SO:0000673	SO:0000673	transcript	SO:0000831
1	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	\N	three_prime_cis_splice_site	SOFA	\N	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	186230	SO:0000676	SO:0000676	canonical_three_prime_splice_site	SO:0000164
1	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	\N	five_prime_cis_splice_site	SOFA	\N	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	186231	SO:0000677	SO:0000677	canonical_five_prime_splice_site	SO:0000163
1	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	\N	three_prime_cis_splice_site	SOFA	\N	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	186232	SO:0000678	SO:0000678	non_canonical_three_prime_splice_site	SO:0000164
1	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	\N	five_prime_cis_splice_site	SOFA	\N	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	186233	SO:0000679	SO:0000679	non_canonical_five_prime_splice_site	SO:0000163
1	"First codon to be translated by a ribosome." [SO:ke]	\N	start_codon	SOFA	\N	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	186234	SO:0000680	SO:0000680	non_canonical_start_codon	SO:0000318
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons." [SO:ke]	SO	186235	SO:0000681	SO:0000681	aberrant_processed_transcript	SO:0000673
1	"Region of a transcript that regulates splicing." [SO:ke]	\N	splice_enhancer	SOFA	\N	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	186236	SO:0000683	SO:0000683	exonic_splice_enhancer	SO:0000344
1	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SOFA	nuclease_binding_site	SOFA	SOFA	sequence	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SO	186237	SO:0000684	SO:0000684	nuclease_sensitive_site	SO:0000059
1	"" []	\N	nuclease_hypersensitive_site	\N	\N	sequence	"" []	SO	186238	SO:0000685	SO:0000685	DNAseI_hypersensitive_site	SO:0000322
1	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	\N	chromosomal_translocation	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	186239	SO:0000686	SO:0000686	translocation_element	SO:1000044
1	"A sequence_feature with an extent of zero." [SO:ke]	SOFA	junction	SOFA	SOFA	sequence	"The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]	SO	186240	SO:0000687	SO:0000687	deletion_junction	SO:0000699
1	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]	SO	186241	SO:0000688	SO:0000688	golden_path	SO:0000353
1	"A match to an EST or cDNA sequence." [SO:ke]	SOFA	expressed_sequence_match	SOFA	SOFA	sequence	"A match against cDNA sequence." [SO:ke]	SO	186242	SO:0000689	SO:0000689	cDNA_match	SO:0000102
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes a polycistronic transcript." [SO:xp]	SO	186243	SO:0000690	SO:0000690	gene_with_polycistronic_transcript	SO:0000704
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	186244	SO:0000691	SO:0000691	cleaved_initiator_methionine	SO:0100011
1	"A gene that encodes a polycistronic transcript." [SO:xp]	\N	gene_with_polycistronic_transcript	\N	\N	sequence	"A gene that encodes a dicistronic transcript." [SO:xp]	SO	186245	SO:0000692	SO:0000692	gene_with_dicistronic_transcript	SO:0000690
1	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene that encodes an mRNA that is recoded." [SO:xp]	SO	186246	SO:0000693	SO:0000693	gene_with_recoded_mRNA	SO:0001217
1	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SOFA	SNV	SOFA	SOFA	sequence	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SO	186247	SO:0000694	SO:0000694	SNP	SO:0001483
1	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A sequence used in experiment." [SO:ke]	SO	186248	SO:0000695	SO:0000695	reagent	SO:0001409
1	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SO	186249	SO:0000696	SO:0000696	oligo	SO:0000695
1	"A gene that encodes an mRNA that is recoded." [SO:xp]	\N	gene_with_recoded_mRNA	\N	\N	sequence	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	SO	186250	SO:0000697	SO:0000697	gene_with_stop_codon_read_through	SO:0000693
1	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	\N	gene_with_stop_codon_read_through	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	186251	SO:0000698	SO:0000698	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0000697
1	"A gene that encodes an mRNA that is recoded." [SO:xp]	\N	gene_with_recoded_mRNA	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	186252	SO:0000698	SO:0000698	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0000693
1	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence_feature with an extent of zero." [SO:ke]	SO	186253	SO:0000699	SO:0000699	junction	SO:0000110
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A comment about the sequence." [SO:ke]	SO	186254	SO:0000700	SO:0000700	remark	SO:0001410
1	"A region where the sequence differs from that of a specified sequence." [SO:ke]	SOFA	sequence_difference	SOFA	SOFA	sequence	"A region of sequence where the validity of the base calling is questionable." [SO:ke]	SO	186255	SO:0000701	SO:0000701	possible_base_call_error	SO:0000413
1	"A region where the sequence differs from that of a specified sequence." [SO:ke]	SOFA	sequence_difference	SOFA	SOFA	sequence	"A region of sequence where there may have been an error in the assembly." [SO:ke]	SO	186256	SO:0000702	SO:0000702	possible_assembly_error	SO:0000413
1	"A comment about the sequence." [SO:ke]	SOFA	remark	SOFA	SOFA	sequence	"A region of sequence implicated in an experimental result." [SO:ke]	SO	186257	SO:0000703	SO:0000703	experimental_result_region	SO:0000700
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	SO	186258	SO:0000704	SO:0000704	gene	SO:0001411
1	"A region of sequence containing one or more repeat units." [SO:ke]	SOFA	repeat_region	SOFA	SOFA	sequence	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SO	186259	SO:0000705	SO:0000705	tandem_repeat	SO:0000657
1	"Primary transcript region bordering trans-splice junction." [SO:ke]	SOFA	trans_splice_site	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	186260	SO:0000706	SO:0000706	trans_splice_acceptor_site	SO:0001420
1	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	\N	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	186261	SO:0000707	SO:0000707	trans_splice_donor_site	SO:0001420
1	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	186262	SO:0000708	SO:0000708	SL1_acceptor_site	SO:0000706
1	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	186263	SO:0000709	SO:0000709	SL2_acceptor_site	SO:0000706
1	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	\N	gene_with_stop_codon_read_through	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	SO	186264	SO:0000710	SO:0000710	gene_with_stop_codon_redefined_as_selenocysteine	SO:0000697
1	"A gene that encodes an mRNA that is recoded." [SO:xp]	\N	gene_with_recoded_mRNA	\N	\N	sequence	"A gene with mRNA recoded by translational bypass." [SO:xp]	SO	186265	SO:0000711	SO:0000711	gene_with_mRNA_recoded_by_translational_bypass	SO:0000693
1	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene with mRNA recoded by translational bypass." [SO:xp]	SO	186266	SO:0000711	SO:0000711	gene_with_mRNA_recoded_by_translational_bypass	SO:0001217
1	"A gene that encodes an mRNA that is recoded." [SO:xp]	\N	gene_with_recoded_mRNA	\N	\N	sequence	"A gene encoding a transcript that has a translational frameshift." [SO:xp]	SO	186267	SO:0000712	SO:0000712	gene_with_transcript_with_translational_frameshift	SO:0000693
1	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A motif that is active in the DNA form of the sequence." [SO:ke]	SO	186268	SO:0000713	SO:0000713	DNA_motif	SO:0000714
1	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	SOFA	sequence_motif	SOFA	SOFA	sequence	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	SO	186269	SO:0000714	SO:0000714	nucleotide_motif	SO:0001683
1	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	SOFA	nucleotide_motif	SOFA	SOFA	sequence	"A motif that is active in RNA sequence." [SO:ke]	SO	186270	SO:0000715	SO:0000715	RNA_motif	SO:0000714
1	"A transcript that is dicistronic." [SO:ke]	\N	dicistronic_transcript	\N	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	186271	SO:0000716	SO:0000716	dicistronic_mRNA	SO:0000079
1	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	\N	polycistronic_mRNA	\N	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	186272	SO:0000716	SO:0000716	dicistronic_mRNA	SO:0000634
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	186273	SO:0000716	SO:0000716	dicistronic_mRNA	SO:0000234
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	SO	186274	SO:0000717	SO:0000717	reading_frame	SO:0001410
1	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	\N	reading_frame	SOFA	\N	sequence	"A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]	SO	186275	SO:0000718	SO:0000718	blocked_reading_frame	SO:0000717
1	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SO	186276	SO:0000719	SO:0000719	ultracontig	SO:0001876
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposable element that is foreign." [SO:ke]	SO	186277	SO:0000720	SO:0000720	foreign_transposable_element	SO:0000101
1	"A gene that encodes a dicistronic transcript." [SO:xp]	\N	gene_with_dicistronic_transcript	\N	\N	sequence	"A gene that encodes a dicistronic primary transcript." [SO:xp]	SO	186278	SO:0000721	SO:0000721	gene_with_dicistronic_primary_transcript	SO:0000692
1	"A gene that encodes a dicistronic transcript." [SO:xp]	\N	gene_with_dicistronic_transcript	\N	\N	sequence	"A gene that encodes a polycistronic mRNA." [SO:xp]	SO	186279	SO:0000722	SO:0000722	gene_with_dicistronic_mRNA	SO:0000692
1	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]	SO	186280	SO:0000723	SO:0000723	iDNA	SO:0000298
1	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	origin_of_replication	SOFA	SOFA	sequence	"A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	186281	SO:0000724	SO:0000724	oriT	SO:0000296
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	biosapiens,SOFA	peptide_localization_signal	SOFA	biosapiens,SOFA	sequence	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	186282	SO:0000725	SO:0000725	transit_peptide	SO:0001527
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"The simplest repeated component of a repeat region. A single repeat." [SO:ke]	SO	186283	SO:0000726	SO:0000726	repeat_unit	SO:0001411
1	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SOFA	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SO	186284	SO:0000727	SO:0000727	CRM	SO:0001055
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	\N	cleaved_peptide_region	biosapiens,SOFA	\N	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	186285	SO:0000728	SO:0000728	intein	SO:0100011
1	"" []	\N	protein_coding	\N	\N	sequence	"An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]	SO	186286	SO:0000729	SO:0000729	intein_containing	SO:0000010
1	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SO	186287	SO:0000730	SO:0000730	gap	SO:0000143
1	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SO	186288	SO:0000730	SO:0000730	gap	SO:0000353
1	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute to describe a feature that is incomplete." [SO:ke]	SO	186289	SO:0000731	SO:0000731	fragmentary	SO:0000905
1	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute describing an unverified region." [SO:ke]	SO	186290	SO:0000732	SO:0000732	predicted	SO:0000905
1	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a located_sequence_feature." [SO:ke]	SO	186291	SO:0000733	SO:0000733	feature_attribute	SO:0000400
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	186292	SO:0000734	SO:0000734	exemplar_mRNA	SO:0000234
1	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	186293	SO:0000735	SO:0000735	sequence_location	SO:0000400
1	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	186294	SO:0000736	SO:0000736	organelle_sequence	SO:0000735
1	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	186295	SO:0000737	SO:0000737	mitochondrial_sequence	SO:0000736
1	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	186296	SO:0000738	SO:0000738	nuclear_sequence	SO:0000736
1	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	186297	SO:0000739	SO:0000739	nucleomorphic_sequence	SO:0000736
1	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	186298	SO:0000740	SO:0000740	plastid_sequence	SO:0000736
1	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055]	SO	186299	SO:0000741	SO:0000741	kinetoplast	SO:0001026
1	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055]	SO	186300	SO:0000741	SO:0000741	kinetoplast	SO:0001260
1	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]	SO	186301	SO:0000742	SO:0000742	maxicircle	SO:0001235
1	"" []	\N	plastid_sequence	\N	\N	sequence	"" []	SO	186302	SO:0000743	SO:0000743	apicoplast_sequence	SO:0000740
1	"" []	\N	plastid_sequence	\N	\N	sequence	"" []	SO	186303	SO:0000744	SO:0000744	chromoplast_sequence	SO:0000740
1	"" []	\N	plastid_sequence	\N	\N	sequence	"" []	SO	186304	SO:0000745	SO:0000745	chloroplast_sequence	SO:0000740
1	"" []	\N	plastid_sequence	\N	\N	sequence	"" []	SO	186305	SO:0000746	SO:0000746	cyanelle_sequence	SO:0000740
1	"" []	\N	plastid_sequence	\N	\N	sequence	"" []	SO	186306	SO:0000747	SO:0000747	leucoplast_sequence	SO:0000740
1	"" []	\N	plastid_sequence	\N	\N	sequence	"" []	SO	186307	SO:0000748	SO:0000748	proplastid_sequence	SO:0000740
1	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	186308	SO:0000749	SO:0000749	plasmid_location	SO:0000735
1	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	origin_of_replication	SOFA	\N	sequence	"An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]	SO	186309	SO:0000750	SO:0000750	amplification_origin	SO:0000296
1	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	186310	SO:0000751	SO:0000751	proviral_location	SO:0000735
1	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	186311	SO:0000752	SO:0000752	gene_group_regulatory_region	SO:0001679
1	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SO	186312	SO:0000753	SO:0000753	clone_insert	SO:0000695
1	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SOFA	clone	SOFA	SOFA	sequence	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SO	186313	SO:0000753	SO:0000753	clone_insert	SO:0000151
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	186314	SO:0000754	SO:0000754	lambda_vector	SO:0000440
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"" []	SO	186315	SO:0000755	SO:0000755	plasmid_vector	SO:0000440
1	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"" []	SO	186316	SO:0000755	SO:0000755	plasmid_vector	SO:0001235
1	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	\N	DNA	\N	\N	sequence	"DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]	SO	186317	SO:0000756	SO:0000756	cDNA	SO:0000352
1	"DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]	\N	cDNA	\N	\N	sequence	"" []	SO	186318	SO:0000757	SO:0000757	single_stranded_cDNA	SO:0000756
1	"DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]	\N	cDNA	\N	\N	sequence	"" []	SO	186319	SO:0000758	SO:0000758	double_stranded_cDNA	SO:0000756
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	186320	SO:0000766	SO:0000766	pyrrolysyl_tRNA	SO:0000253
1	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"A plasmid that may integrate with a chromosome." [SO:ma]	SO	186321	SO:0000768	SO:0000768	episome	SO:0000155
1	"A region of a tmRNA." [SO:cb]	\N	tmRNA_region	\N	\N	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	186322	SO:0000769	SO:0000769	tmRNA_coding_piece	SO:0000847
1	"A region of a tmRNA." [SO:cb]	\N	tmRNA_region	\N	\N	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	186323	SO:0000770	SO:0000770	tmRNA_acceptor_piece	SO:0000847
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]	SO	186324	SO:0000771	SO:0000771	QTL	SO:0001411
1	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	SO	186325	SO:0000772	SO:0000772	genomic_island	SO:0001039
1	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	\N	genomic_island	\N	\N	sequence	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	SO	186326	SO:0000773	SO:0000773	pathogenic_island	SO:0000772
1	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	\N	genomic_island	\N	\N	sequence	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	186327	SO:0000774	SO:0000774	metabolic_island	SO:0000772
1	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	\N	genomic_island	\N	\N	sequence	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	SO	186328	SO:0000775	SO:0000775	adaptive_island	SO:0000772
1	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	\N	genomic_island	\N	\N	sequence	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	186329	SO:0000776	SO:0000776	symbiosis_island	SO:0000772
1	"A non-functional descendant of a functional entity." [SO:cjm]	SOFA	pseudogenic_region	SOFA	SOFA	sequence	"A non functional descendant of an rRNA." [SO:ke]	SO	186330	SO:0000777	SO:0000777	pseudogenic_rRNA	SO:0000462
1	"A non-functional descendant of a functional entity." [SO:cjm]	SOFA	pseudogenic_region	SOFA	SOFA	sequence	"A non functional descendent of a tRNA." [SO:ke]	SO	186331	SO:0000778	SO:0000778	pseudogenic_tRNA	SO:0000462
1	"A plasmid that is engineered." [SO:xp]	\N	engineered_plasmid	\N	\N	sequence	"An episome that is engineered." [SO:xp]	SO	186332	SO:0000779	SO:0000779	engineered_episome	SO:0000637
1	"A plasmid that may integrate with a chromosome." [SO:ma]	\N	episome	\N	\N	sequence	"An episome that is engineered." [SO:xp]	SO	186333	SO:0000779	SO:0000779	engineered_episome	SO:0000768
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Attribute describing sequence that has been integrated with foreign sequence." [SO:ke]	SO	186334	SO:0000781	SO:0000781	transgenic	SO:0000733
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a feature that occurs in nature." [SO:ke]	SO	186335	SO:0000782	SO:0000782	natural	SO:0000733
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a region that was modified in vitro." [SO:ke]	SO	186336	SO:0000783	SO:0000783	engineered	SO:0000733
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a region from another species." [SO:ke]	SO	186337	SO:0000784	SO:0000784	foreign	SO:0000733
1	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	\N	sequence	"" []	SO	186338	SO:0000785	SO:0000785	cloned_region	SO:0000695
1	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	\N	clone_insert	SOFA	\N	sequence	"" []	SO	186339	SO:0000785	SO:0000785	cloned_region	SO:0000753
1	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute to describe a feature that has been proven." [SO:ke]	SO	186340	SO:0000789	SO:0000789	validated	SO:0000905
1	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute describing a feature that is invalidated." [SO:ke]	SO	186341	SO:0000790	SO:0000790	invalidated	SO:0000905
1	"A region that rescues." [SO:xp]	\N	rescue_region	\N	\N	sequence	"A rescue region that is engineered." [SO:xp]	SO	186342	SO:0000794	SO:0000794	engineered_rescue_region	SO:0000411
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A rescue region that is engineered." [SO:xp]	SO	186343	SO:0000794	SO:0000794	engineered_rescue_region	SO:0000804
1	"By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]	\N	mini_gene	\N	\N	sequence	"A mini_gene that rescues." [SO:xp]	SO	186344	SO:0000795	SO:0000795	rescue_mini_gene	SO:0000815
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	SO	186345	SO:0000796	SO:0000796	transgenic_transposable_element	SO:0000101
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	186346	SO:0000797	SO:0000797	natural_transposable_element	SO:0000101
1	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	186347	SO:0000797	SO:0000797	natural_transposable_element	SO:0001038
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	186348	SO:0000798	SO:0000798	engineered_transposable_element	SO:0000101
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	186349	SO:0000798	SO:0000798	engineered_transposable_element	SO:0000804
1	"A transposable element that is foreign." [SO:ke]	\N	foreign_transposable_element	\N	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	186350	SO:0000799	SO:0000799	engineered_foreign_transposable_element	SO:0000720
1	"TE that has been modified by manipulations in vitro." [FB:mc]	\N	engineered_transposable_element	\N	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	186351	SO:0000799	SO:0000799	engineered_foreign_transposable_element	SO:0000798
1	"A region that is engineered and foreign." [SO:xp]	\N	engineered_foreign_region	\N	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	186352	SO:0000799	SO:0000799	engineered_foreign_transposable_element	SO:0000805
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	186353	SO:0000799	SO:0000799	engineered_foreign_transposable_element	SO:0000101
1	"A chromosome variation derived from an event during meiosis." [SO:ke]	\N	assortment_derived_variation	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	186354	SO:0000800	SO:0000800	assortment_derived_duplication	SO:0001504
1	"A chromosome variation derived from an event during meiosis." [SO:ke]	\N	assortment_derived_variation	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	186355	SO:0000801	SO:0000801	assortment_derived_deficiency_plus_duplication	SO:0001504
1	"A chromosome variation derived from an event during meiosis." [SO:ke]	\N	assortment_derived_variation	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	186356	SO:0000802	SO:0000802	assortment_derived_deficiency	SO:0001504
1	"A chromosome variation derived from an event during meiosis." [SO:ke]	\N	assortment_derived_variation	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	186357	SO:0000803	SO:0000803	assortment_derived_aneuploid	SO:0001504
1	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A region that is engineered." [SO:xp]	SO	186358	SO:0000804	SO:0000804	engineered_region	SO:0001409
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A region that is engineered." [SO:xp]	SO	186359	SO:0000804	SO:0000804	engineered_region	SO:0000001
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A region that is engineered and foreign." [SO:xp]	SO	186360	SO:0000805	SO:0000805	engineered_foreign_region	SO:0000804
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A region that is engineered and foreign." [SO:xp]	SO	186361	SO:0000805	SO:0000805	engineered_foreign_region	SO:0000001
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	186362	SO:0000806	SO:0000806	fusion	SO:0000733
1	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	\N	sequence	"A tag that is engineered." [SO:xp]	SO	186363	SO:0000807	SO:0000807	engineered_tag	SO:0000324
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A tag that is engineered." [SO:xp]	SO	186364	SO:0000807	SO:0000807	engineered_tag	SO:0000804
1	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	\N	cDNA_clone	\N	\N	sequence	"A cDNA clone that has been validated." [SO:xp]	SO	186365	SO:0000808	SO:0000808	validated_cDNA_clone	SO:0000317
1	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	\N	cDNA_clone	\N	\N	sequence	"A cDNA clone that is invalid." [SO:xp]	SO	186366	SO:0000809	SO:0000809	invalidated_cDNA_clone	SO:0000317
1	"A cDNA clone that is invalid." [SO:xp]	\N	invalidated_cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated because it is chimeric." [SO:xp]	SO	186367	SO:0000810	SO:0000810	chimeric_cDNA_clone	SO:0000809
1	"A cDNA clone that is invalid." [SO:xp]	\N	invalidated_cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated by genomic contamination." [SO:xp]	SO	186368	SO:0000811	SO:0000811	genomically_contaminated_cDNA_clone	SO:0000809
1	"A cDNA clone that is invalid." [SO:xp]	\N	invalidated_cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated by polyA priming." [SO:xp]	SO	186369	SO:0000812	SO:0000812	polyA_primed_cDNA_clone	SO:0000809
1	"A cDNA clone that is invalid." [SO:xp]	\N	invalidated_cDNA_clone	\N	\N	sequence	"A cDNA invalidated clone by partial processing." [SO:xp]	SO	186370	SO:0000813	SO:0000813	partially_processed_cDNA_clone	SO:0000809
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]	SO	186371	SO:0000814	SO:0000814	rescue	SO:0000733
1	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	\N	ORF	SOFA	\N	sequence	"By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]	SO	186372	SO:0000815	SO:0000815	mini_gene	SO:0000236
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that rescues." [SO:xp]	SO	186373	SO:0000816	SO:0000816	rescue_gene	SO:0000704
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]	SO	186374	SO:0000817	SO:0000817	wild_type	SO:0000733
1	"A gene that rescues." [SO:xp]	\N	rescue_gene	\N	\N	sequence	"A gene that rescues." [SO:xp]	SO	186375	SO:0000818	SO:0000818	wild_type_rescue_gene	SO:0000816
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that rescues." [SO:xp]	SO	186376	SO:0000818	SO:0000818	wild_type_rescue_gene	SO:0000704
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in a mitochondria." [SO:xp]	SO	186377	SO:0000819	SO:0000819	mitochondrial_chromosome	SO:0000340
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in a chloroplast." [SO:xp]	SO	186378	SO:0000820	SO:0000820	chloroplast_chromosome	SO:0000340
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in a chromoplast." [SO:xp]	SO	186379	SO:0000821	SO:0000821	chromoplast_chromosome	SO:0000340
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in a cyanelle." [SO:xp]	SO	186380	SO:0000822	SO:0000822	cyanelle_chromosome	SO:0000340
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome with origin in a leucoplast." [SO:xp]	SO	186381	SO:0000823	SO:0000823	leucoplast_chromosome	SO:0000340
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in a macronucleus." [SO:xp]	SO	186382	SO:0000824	SO:0000824	macronuclear_chromosome	SO:0000340
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in a micronucleus." [SO:xp]	SO	186383	SO:0000825	SO:0000825	micronuclear_chromosome	SO:0000340
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in a nucleus." [SO:xp]	SO	186384	SO:0000828	SO:0000828	nuclear_chromosome	SO:0000340
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in a nucleomorph." [SO:xp]	SO	186385	SO:0000829	SO:0000829	nucleomorphic_chromosome	SO:0000340
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a chromosome." [SO:ke]	SO	186386	SO:0000830	SO:0000830	chromosome_part	SO:0001411
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SOFA	chromosome	SOFA	SOFA	sequence	"A region of a chromosome." [SO:ke]	SO	186387	SO:0000830	SO:0000830	chromosome_part	SO:0000340
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a gene." [SO:ke]	SO	186388	SO:0000831	SO:0000831	gene_member_region	SO:0001411
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a transcript." [SO:ke]	SO	186389	SO:0000833	SO:0000833	transcript_region	SO:0001411
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of a transcript." [SO:ke]	SO	186390	SO:0000833	SO:0000833	transcript_region	SO:0000673
1	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region of a mature transcript." [SO:ke]	SO	186391	SO:0000834	SO:0000834	mature_transcript_region	SO:0000833
1	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	186392	SO:0000835	SO:0000835	primary_transcript_region	SO:0000833
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	186393	SO:0000835	SO:0000835	primary_transcript_region	SO:0000185
1	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	186394	SO:0000836	SO:0000836	mRNA_region	SO:0000834
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	186395	SO:0000836	SO:0000836	mRNA_region	SO:0000234
1	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	186396	SO:0000837	SO:0000837	UTR_region	SO:0000836
1	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	186397	SO:0000838	SO:0000838	rRNA_primary_transcript_region	SO:0000835
1	"A primary transcript encoding a ribosomal RNA." [SO:ke]	\N	rRNA_primary_transcript	SOFA	\N	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	186398	SO:0000838	SO:0000838	rRNA_primary_transcript_region	SO:0000209
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	SO	186399	SO:0000839	SO:0000839	polypeptide_region	SO:0001411
1	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens,SOFA	polypeptide	SOFA	biosapiens,SOFA	sequence	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	SO	186400	SO:0000839	SO:0000839	polypeptide_region	SO:0000104
1	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"A region of a repeated sequence." [SO:ke]	SO	186401	SO:0000840	SO:0000840	repeat_component	SO:0001412
1	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	186402	SO:0000841	SO:0000841	spliceosomal_intron_region	SO:0000835
1	"An intron which is spliced by the spliceosome." [SO:ke]	SOFA	spliceosomal_intron	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	186403	SO:0000841	SO:0000841	spliceosomal_intron_region	SO:0000662
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"" []	SO	186404	SO:0000842	SO:0000842	gene_component_region	SO:0001411
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	SOFA	gene	SOFA	SOFA	sequence	"" []	SO	186405	SO:0000842	SO:0000842	gene_component_region	SO:0000704
1	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"A region of a tmRNA." [SO:cb]	SO	186406	SO:0000847	SO:0000847	tmRNA_region	SO:0000834
1	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	\N	tmRNA	\N	\N	sequence	"A region of a tmRNA." [SO:cb]	SO	186407	SO:0000847	SO:0000847	tmRNA_region	SO:0000584
1	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	186408	SO:0000848	SO:0000848	LTR_component	SO:0000840
1	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	186409	SO:0000848	SO:0000848	LTR_component	SO:0000286
1	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	186410	SO:0000849	SO:0000849	three_prime_LTR_component	SO:0000848
1	"" []	\N	three_prime_LTR	\N	\N	sequence	"" []	SO	186411	SO:0000849	SO:0000849	three_prime_LTR_component	SO:0000426
1	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	186412	SO:0000850	SO:0000850	five_prime_LTR_component	SO:0000848
1	"" []	\N	five_prime_LTR	\N	\N	sequence	"" []	SO	186413	SO:0000850	SO:0000850	five_prime_LTR_component	SO:0000425
1	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	186414	SO:0000851	SO:0000851	CDS_region	SO:0000836
1	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SOFA	CDS	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	186415	SO:0000851	SO:0000851	CDS_region	SO:0000316
1	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	186416	SO:0000852	SO:0000852	exon_region	SO:0000833
1	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	186417	SO:0000852	SO:0000852	exon_region	SO:0000147
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A region that is homologous to another region." [SO:ke]	SO	186418	SO:0000853	SO:0000853	homologous_region	SO:0000330
1	"A region that is homologous to another region." [SO:ke]	\N	homologous_region	\N	\N	sequence	"A homologous_region that is paralogous to another region." [SO:ke]	SO	186419	SO:0000854	SO:0000854	paralogous_region	SO:0000853
1	"A region that is homologous to another region." [SO:ke]	\N	homologous_region	\N	\N	sequence	"A homologous_region that is orthologous to another region." [SO:ke]	SO	186420	SO:0000855	SO:0000855	orthologous_region	SO:0000853
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	186421	SO:0000856	SO:0000856	conserved	SO:0000733
1	"" []	\N	conserved	\N	\N	sequence	"Similarity due to common ancestry." [SO:ke]	SO	186422	SO:0000857	SO:0000857	homologous	SO:0000856
1	"Similarity due to common ancestry." [SO:ke]	\N	homologous	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]	SO	186423	SO:0000858	SO:0000858	orthologous	SO:0000857
1	"Similarity due to common ancestry." [SO:ke]	\N	homologous	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]	SO	186424	SO:0000859	SO:0000859	paralogous	SO:0000857
1	"" []	\N	conserved	\N	\N	sequence	"Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]	SO	186425	SO:0000860	SO:0000860	syntenic	SO:0000856
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"A primary transcript that is capped." [SO:xp]	SO	186426	SO:0000861	SO:0000861	capped_primary_transcript	SO:0000185
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA that is capped." [SO:xp]	SO	186427	SO:0000862	SO:0000862	capped_mRNA	SO:0000234
1	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing an mRNA feature." [SO:ke]	SO	186428	SO:0000863	SO:0000863	mRNA_attribute	SO:0000237
1	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]	SO	186429	SO:0000864	SO:0000864	exemplar	SO:0000863
1	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	SO	186430	SO:0000865	SO:0000865	frameshift	SO:0000863
1	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	\N	frameshift	\N	\N	sequence	"A frameshift caused by deleting one base." [SO:ke]	SO	186431	SO:0000866	SO:0000866	minus_1_frameshift	SO:0000865
1	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	\N	frameshift	\N	\N	sequence	"A frameshift caused by deleting two bases." [SO:ke]	SO	186432	SO:0000867	SO:0000867	minus_2_frameshift	SO:0000865
1	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	\N	frameshift	\N	\N	sequence	"A frameshift caused by inserting one base." [SO:ke]	SO	186433	SO:0000868	SO:0000868	plus_1_frameshift	SO:0000865
1	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	\N	frameshift	\N	\N	sequence	"A frameshift caused by inserting two bases." [SO:ke]	SO	186434	SO:0000869	SO:0000869	plus_2_framshift	SO:0000865
1	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]	SO	186435	SO:0000870	SO:0000870	trans_spliced	SO:0000237
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA that is polyadenylated." [SO:xp]	SO	186436	SO:0000871	SO:0000871	polyadenylated_mRNA	SO:0000234
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	186437	SO:0000872	SO:0000872	trans_spliced_mRNA	SO:0000234
1	"A transcript that is trans-spliced." [SO:xp]	\N	trans_spliced_transcript	\N	\N	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	186438	SO:0000872	SO:0000872	trans_spliced_mRNA	SO:0000479
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is edited." [SO:ke]	SO	186439	SO:0000873	SO:0000873	edited_transcript	SO:0000673
1	"A transcript that is edited." [SO:ke]	\N	edited_transcript	\N	\N	sequence	"A transcript that has been edited by A to I substitution." [SO:ke]	SO	186440	SO:0000874	SO:0000874	edited_transcript_by_A_to_I_substitution	SO:0000873
1	"An attribute describing a sequence that is bound by another molecule." [SO:ke]	\N	bound_by_factor	\N	\N	sequence	"An attribute describing a sequence that is bound by a protein." [SO:ke]	SO	186441	SO:0000875	SO:0000875	bound_by_protein	SO:0000277
1	"An attribute describing a sequence that is bound by another molecule." [SO:ke]	\N	bound_by_factor	\N	\N	sequence	"An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]	SO	186442	SO:0000876	SO:0000876	bound_by_nucleic_acid	SO:0000277
1	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]	SO	186443	SO:0000877	SO:0000877	alternatively_spliced	SO:0000237
1	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for one gene product." [SO:ke]	SO	186444	SO:0000878	SO:0000878	monocistronic	SO:0000237
1	"An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]	\N	polycistronic	\N	\N	sequence	"An attribute describing a sequence that contains the code for two gene products." [SO:ke]	SO	186445	SO:0000879	SO:0000879	dicistronic	SO:0000880
1	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]	SO	186446	SO:0000880	SO:0000880	polycistronic	SO:0000237
1	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	SO	186447	SO:0000881	SO:0000881	recoded	SO:0000863
1	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	\N	recoded	\N	\N	sequence	"An attribute describing the alteration of codon meaning." [SO:ke]	SO	186448	SO:0000882	SO:0000882	codon_redefined	SO:0000881
1	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	\N	recoded_codon	\N	\N	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	186449	SO:0000883	SO:0000883	stop_codon_read_through	SO:0000145
1	"A stop codon redefined to be a new amino acid." [SO:ke]	\N	stop_codon_read_through	\N	\N	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	186450	SO:0000884	SO:0000884	stop_codon_redefined_as_pyrrolysine	SO:0000883
1	"A stop codon redefined to be a new amino acid." [SO:ke]	\N	stop_codon_read_through	\N	\N	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	186451	SO:0000885	SO:0000885	stop_codon_redefined_as_selenocysteine	SO:0000883
1	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	\N	recoded	\N	\N	sequence	"Recoded mRNA where a block of nucleotides is not translated." [SO:ke]	SO	186452	SO:0000886	SO:0000886	recoded_by_translational_bypass	SO:0000881
1	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	\N	recoded	\N	\N	sequence	"Recoding by frameshifting a particular site." [SO:ke]	SO	186453	SO:0000887	SO:0000887	translationally_frameshifted	SO:0000881
1	"A gene that is epigenetically modified." [SO:ke]	\N	epigenetically_modified_gene	\N	\N	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	186454	SO:0000888	SO:0000888	maternally_imprinted_gene	SO:0000898
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	186455	SO:0000888	SO:0000888	maternally_imprinted_gene	SO:0000704
1	"A gene that is epigenetically modified." [SO:ke]	\N	epigenetically_modified_gene	\N	\N	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	186456	SO:0000889	SO:0000889	paternally_imprinted_gene	SO:0000898
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	186457	SO:0000889	SO:0000889	paternally_imprinted_gene	SO:0000704
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is post translationally regulated." [SO:xp]	SO	186458	SO:0000890	SO:0000890	post_translationally_regulated_gene	SO:0000704
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is negatively autoreguated." [SO:xp]	SO	186459	SO:0000891	SO:0000891	negatively_autoregulated_gene	SO:0000704
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is positively autoregulated." [SO:xp]	SO	186460	SO:0000892	SO:0000892	positively_autoregulated_gene	SO:0000704
1	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	SO	186461	SO:0000893	SO:0000893	silenced	SO:0000126
1	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	\N	silenced	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	SO	186462	SO:0000894	SO:0000894	silenced_by_DNA_modification	SO:0000893
1	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	\N	silenced_by_DNA_modification	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	186463	SO:0000895	SO:0000895	silenced_by_DNA_methylation	SO:0000894
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is translationally regulated." [SO:xp]	SO	186464	SO:0000896	SO:0000896	translationally_regulated_gene	SO:0000704
1	"A gene that is epigenetically modified." [SO:ke]	\N	epigenetically_modified_gene	\N	\N	sequence	"A gene that is allelically_excluded." [SO:xp]	SO	186465	SO:0000897	SO:0000897	allelically_excluded_gene	SO:0000898
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is epigenetically modified." [SO:ke]	SO	186466	SO:0000898	SO:0000898	epigenetically_modified_gene	SO:0000704
1	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A gene that is epigenetically modified." [SO:ke]	SO	186467	SO:0000898	SO:0000898	epigenetically_modified_gene	SO:0001720
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]	SO	186468	SO:0000902	SO:0000902	transgene	SO:0000704
1	"" []	\N	proviral_location	\N	\N	sequence	"" []	SO	186469	SO:0000903	SO:0000903	endogenous_retroviral_sequence	SO:0000751
1	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	\N	epigenetically_modified	\N	\N	sequence	"An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]	SO	186470	SO:0000904	SO:0000904	rearranged_at_DNA_level	SO:0000133
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	SO	186471	SO:0000905	SO:0000905	status	SO:0000733
1	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"Attribute to describe a feature that is independently known - not predicted." [SO:ke]	SO	186472	SO:0000906	SO:0000906	independently_known	SO:0000905
1	"An attribute describing an unverified region." [SO:ke]	\N	predicted	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]	SO	186473	SO:0000907	SO:0000907	supported_by_sequence_similarity	SO:0000732
1	"An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]	\N	supported_by_sequence_similarity	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]	SO	186474	SO:0000908	SO:0000908	supported_by_domain_match	SO:0000907
1	"An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]	\N	supported_by_sequence_similarity	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]	SO	186475	SO:0000909	SO:0000909	supported_by_EST_or_cDNA	SO:0000907
1	"An attribute describing an unverified region." [SO:ke]	\N	predicted	\N	\N	sequence	"" []	SO	186476	SO:0000910	SO:0000910	orphan	SO:0000732
1	"An attribute describing an unverified region." [SO:ke]	\N	predicted	\N	\N	sequence	"An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]	SO	186477	SO:0000911	SO:0000911	predicted_by_ab_initio_computation	SO:0000732
1	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186478	SO:0000912	SO:0000912	asx_turn	SO:0001128
1	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	\N	clone_insert	SOFA	\N	sequence	"A clone insert made from cDNA." [SO:xp]	SO	186479	SO:0000913	SO:0000913	cloned_cDNA_insert	SO:0000753
1	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	\N	clone_insert	SOFA	\N	sequence	"A clone insert made from genomic DNA." [SO:xp]	SO	186480	SO:0000914	SO:0000914	cloned_genomic_insert	SO:0000753
1	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	\N	clone_insert	SOFA	\N	sequence	"A clone insert that is engineered." [SO:xp]	SO	186481	SO:0000915	SO:0000915	engineered_insert	SO:0000753
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A clone insert that is engineered." [SO:xp]	SO	186482	SO:0000915	SO:0000915	engineered_insert	SO:0000804
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA that is edited." [SO:xp]	SO	186483	SO:0000929	SO:0000929	edited_mRNA	SO:0000234
1	"A transcript that is edited." [SO:ke]	\N	edited_transcript	\N	\N	sequence	"An mRNA that is edited." [SO:xp]	SO	186484	SO:0000929	SO:0000929	edited_mRNA	SO:0000873
1	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"A region of guide RNA." [SO:ma]	SO	186485	SO:0000930	SO:0000930	guide_RNA_region	SO:0000834
1	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	\N	guide_RNA	SOFA	\N	sequence	"A region of guide RNA." [SO:ma]	SO	186486	SO:0000930	SO:0000930	guide_RNA_region	SO:0000602
1	"A region of guide RNA." [SO:ma]	\N	guide_RNA_region	\N	\N	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	186487	SO:0000931	SO:0000931	anchor_region	SO:0000930
1	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	\N	protein_coding_primary_transcript	SOFA	\N	sequence	"" []	SO	186488	SO:0000932	SO:0000932	pre_edited_mRNA	SO:0000120
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature between stages of processing." [SO:ke]	SO	186489	SO:0000933	SO:0000933	intermediate	SO:0000733
1	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	\N	nucleotide_binding_site	\N	\N	sequence	"A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]	SO	186490	SO:0000934	SO:0000934	miRNA_target_site	SO:0001655
1	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is edited." [SO:xp]	SO	186491	SO:0000935	SO:0000935	edited_CDS	SO:0000316
1	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	186492	SO:0000936	SO:0000936	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000301
1	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	186493	SO:0000938	SO:0000938	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000301
1	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	186494	SO:0000939	SO:0000939	vertebrate_immune_system_gene_recombination_signal_feature	SO:0000301
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	186495	SO:0000940	SO:0000940	recombinationally_rearranged	SO:0000733
1	"A gene that is recombinationally rearranged." [SO:ke]	\N	recombinationally_rearranged_gene	\N	\N	sequence	"A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]	SO	186496	SO:0000941	SO:0000941	recombinationally_rearranged_vertebrate_immune_system_gene	SO:0000456
1	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	\N	integration_excision_site	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	186497	SO:0000942	SO:0000942	attP_site	SO:0000946
1	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	\N	phage_sequence	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	186498	SO:0000942	SO:0000942	attP_site	SO:0001042
1	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	\N	integration_excision_site	\N	\N	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	186499	SO:0000943	SO:0000943	attB_site	SO:0000946
1	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	\N	integration_excision_site	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	186500	SO:0000944	SO:0000944	attL_site	SO:0000946
1	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	\N	integration_excision_site	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	186501	SO:0000945	SO:0000945	attR_site	SO:0000946
1	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	SO	186502	SO:0000946	SO:0000946	integration_excision_site	SO:0000342
1	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	SO	186503	SO:0000947	SO:0000947	resolution_site	SO:0000342
1	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	SO	186504	SO:0000948	SO:0000948	inversion_site	SO:0000342
1	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	\N	resolution_site	\N	\N	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	186505	SO:0000949	SO:0000949	dif_site	SO:0000947
1	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	\N	integration_excision_site	\N	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	186506	SO:0000950	SO:0000950	attC_site	SO:0000946
1	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	\N	integron	\N	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	186507	SO:0000950	SO:0000950	attC_site	SO:0000365
1	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	terminator	SOFA	\N	sequence	"" []	SO	186508	SO:0000951	SO:0000951	eukaryotic_terminator	SO:0000141
1	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	origin_of_replication	SOFA	\N	sequence	"An origin of vegetative replication in plasmids and phages." [SO:as]	SO	186509	SO:0000952	SO:0000952	oriV	SO:0000296
1	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	origin_of_replication	SOFA	\N	sequence	"An origin of bacterial chromosome replication." [SO:as]	SO	186510	SO:0000953	SO:0000953	oriC	SO:0000296
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	SO	186511	SO:0000954	SO:0000954	DNA_chromosome	SO:0000340
1	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	\N	DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	SO	186512	SO:0000955	SO:0000955	double_stranded_DNA_chromosome	SO:0000954
1	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	\N	DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	SO	186513	SO:0000956	SO:0000956	single_stranded_DNA_chromosome	SO:0000954
1	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	\N	double_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	SO	186514	SO:0000957	SO:0000957	linear_double_stranded_DNA_chromosome	SO:0000955
1	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	\N	double_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	SO	186515	SO:0000958	SO:0000958	circular_double_stranded_DNA_chromosome	SO:0000955
1	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	\N	single_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	SO	186516	SO:0000959	SO:0000959	linear_single_stranded_DNA_chromosome	SO:0000956
1	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	\N	single_stranded_DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	186517	SO:0000960	SO:0000960	circular_single_stranded_DNA_chromosome	SO:0000956
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	SO	186518	SO:0000961	SO:0000961	RNA_chromosome	SO:0000340
1	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	\N	RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	SO	186519	SO:0000962	SO:0000962	single_stranded_RNA_chromosome	SO:0000961
1	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	\N	single_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	SO	186520	SO:0000963	SO:0000963	linear_single_stranded_RNA_chromosome	SO:0000962
1	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	\N	double_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	SO	186521	SO:0000964	SO:0000964	linear_double_stranded_RNA_chromosome	SO:0000965
1	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	\N	RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	SO	186522	SO:0000965	SO:0000965	double_stranded_RNA_chromosome	SO:0000961
1	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	\N	single_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	186523	SO:0000966	SO:0000966	circular_single_stranded_RNA_chromosome	SO:0000962
1	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	\N	double_stranded_RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	SO	186524	SO:0000967	SO:0000967	circular_double_stranded_RNA_chromosome	SO:0000965
1	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	\N	terminal_inverted_repeat_element	\N	\N	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	186525	SO:0000973	SO:0000973	insertion_sequence	SO:0000208
1	"A gene located in kinetoplast sequence." [SO:xp]	\N	kinetoplast_gene	\N	\N	sequence	"" []	SO	186526	SO:0000975	SO:0000975	minicircle_gene	SO:0000089
1	"A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]	\N	minicircle	\N	\N	sequence	"" []	SO	186527	SO:0000975	SO:0000975	minicircle_gene	SO:0000980
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke]	SO	186528	SO:0000976	SO:0000976	cryptic	SO:0000733
1	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	\N	sequence	"" []	SO	186529	SO:0000977	SO:0000977	anchor_binding_site	SO:0000833
1	"A region of guide RNA." [SO:ma]	\N	guide_RNA_region	\N	\N	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	186530	SO:0000978	SO:0000978	template_region	SO:0000930
1	"" []	\N	non_protein_coding	\N	\N	sequence	"A non-protein_coding gene that encodes a guide_RNA." [SO:ma]	SO	186531	SO:0000979	SO:0000979	gRNA_encoding	SO:0000011
1	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]	SO	186532	SO:0000980	SO:0000980	minicircle	SO:0001235
1	"A terminator signal for bacterial transcription." [SO:ke]	\N	bacterial_terminator	\N	\N	sequence	"" []	SO	186533	SO:0000981	SO:0000981	rho_dependent_bacterial_terminator	SO:0000614
1	"A terminator signal for bacterial transcription." [SO:ke]	\N	bacterial_terminator	\N	\N	sequence	"" []	SO	186534	SO:0000982	SO:0000982	rho_independent_bacterial_terminator	SO:0000614
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	186535	SO:0000983	SO:0000983	strand_attribute	SO:0000733
1	"" []	\N	strand_attribute	\N	\N	sequence	"" []	SO	186536	SO:0000984	SO:0000984	single	SO:0000983
1	"" []	\N	strand_attribute	\N	\N	sequence	"" []	SO	186537	SO:0000985	SO:0000985	double	SO:0000983
1	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"" []	SO	186538	SO:0000986	SO:0000986	topology_attribute	SO:0000443
1	"" []	\N	topology_attribute	\N	\N	sequence	"A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]	SO	186539	SO:0000987	SO:0000987	linear	SO:0000986
1	"" []	\N	topology_attribute	\N	\N	sequence	"A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]	SO	186540	SO:0000988	SO:0000988	circular	SO:0000986
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	186541	SO:0000989	SO:0000989	class_II_RNA	SO:0000655
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	186542	SO:0000990	SO:0000990	class_I_RNA	SO:0000655
1	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	\N	DNA	\N	\N	sequence	"" []	SO	186543	SO:0000991	SO:0000991	genomic_DNA	SO:0000352
1	"A clone insert made from genomic DNA." [SO:xp]	\N	cloned_genomic_insert	\N	\N	sequence	"" []	SO	186544	SO:0000992	SO:0000992	BAC_cloned_genomic_insert	SO:0000914
1	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"" []	SO	186545	SO:0000993	SO:0000993	consensus	SO:0000905
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"" []	SO	186546	SO:0000994	SO:0000994	consensus_region	SO:0001410
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"" []	SO	186547	SO:0000994	SO:0000994	consensus_region	SO:0000001
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"" []	SO	186548	SO:0000995	SO:0000995	consensus_mRNA	SO:0000234
1	"" []	\N	consensus_region	\N	\N	sequence	"" []	SO	186549	SO:0000995	SO:0000995	consensus_mRNA	SO:0000994
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	186550	SO:0000996	SO:0000996	predicted_gene	SO:0000704
1	"" []	\N	gene_component_region	SOFA	\N	sequence	"" []	SO	186551	SO:0000997	SO:0000997	gene_fragment	SO:0000842
1	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	\N	cis_splice_site	SOFA	\N	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	186552	SO:0000998	SO:0000998	recursive_splice_site	SO:0001419
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	186553	SO:0000999	SO:0000999	BAC_end	SO:0000150
1	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	\N	BAC	\N	\N	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	186554	SO:0000999	SO:0000999	BAC_end	SO:0000153
1	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SOFA	small_subunit_rRNA	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	186555	SO:0001000	SO:0001000	rRNA_16S	SO:0000650
1	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SOFA	large_subunit_rRNA	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	186556	SO:0001001	SO:0001001	rRNA_23S	SO:0000651
1	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SOFA	large_subunit_rRNA	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	186557	SO:0001002	SO:0001002	rRNA_25S	SO:0000651
1	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	186558	SO:0001003	SO:0001003	solo_LTR	SO:0000286
1	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"" []	SO	186559	SO:0001004	SO:0001004	low_complexity	SO:0000905
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"" []	SO	186560	SO:0001005	SO:0001005	low_complexity_region	SO:0001410
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"" []	SO	186561	SO:0001005	SO:0001005	low_complexity_region	SO:0000001
1	"A viral sequence which has integrated into a host genome." [SO:ke]	\N	proviral_region	SOFA	\N	sequence	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	SO	186562	SO:0001006	SO:0001006	prophage	SO:0000113
1	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	\N	genomic_island	\N	\N	sequence	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	SO	186563	SO:0001007	SO:0001007	cryptic_prophage	SO:0000772
1	"A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	stem_loop	\N	\N	sequence	"A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]	SO	186564	SO:0001008	SO:0001008	tetraloop	SO:0000313
1	"A double stranded oligonucleotide." [SO:ke]	\N	ds_oligo	SOFA	\N	sequence	"A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	SO	186565	SO:0001009	SO:0001009	DNA_constraint_sequence	SO:0000442
1	"A folded DNA sequence." [SO:ke]	\N	DNA_sequence_secondary_structure	\N	\N	sequence	"A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]	SO	186566	SO:0001010	SO:0001010	i_motif	SO:0000142
1	"An oligo composed of synthetic nucleotides." [SO:ke]	\N	synthetic_oligo	\N	\N	sequence	"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]	SO	186567	SO:0001011	SO:0001011	PNA_oligo	SO:0001247
1	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"A DNA sequence with catalytic activity." [SO:cb]	SO	186568	SO:0001012	SO:0001012	DNAzyme	SO:0000696
1	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	\N	MNV	\N	\N	sequence	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	SO	186569	SO:0001013	SO:0001013	MNP	SO:0002007
1	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"" []	SO	186570	SO:0001014	SO:0001014	intron_domain	SO:0000835
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"" []	SO	186571	SO:0001014	SO:0001014	intron_domain	SO:0000188
1	"" []	\N	base_pair	\N	\N	sequence	"A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]	SO	186572	SO:0001015	SO:0001015	wobble_base_pair	SO:0000028
1	"" []	\N	intron_domain	\N	\N	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	186573	SO:0001016	SO:0001016	internal_guide_sequence	SO:0001014
1	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	\N	group_I_intron	SOFA	\N	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	186574	SO:0001016	SO:0001016	internal_guide_sequence	SO:0000587
1	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke]	SO	186575	SO:0001017	SO:0001017	silent_mutation	SO:0001878
1	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]	SO	186576	SO:0001018	SO:0001018	epitope	SO:0000409
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SOFA	sequence_alteration	SOFA	SOFA	sequence	"A variation that increases or decreases the copy number of a given region." [SO:ke]	SO	186577	SO:0001019	SO:0001019	copy_number_variation	SO:0001059
1	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"" []	SO	186578	SO:0001021	SO:0001021	chromosome_breakpoint	SO:0000699
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"" []	SO	186579	SO:0001021	SO:0001021	chromosome_breakpoint	SO:0000340
1	"" []	\N	chromosome_breakpoint	\N	\N	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	186580	SO:0001022	SO:0001022	inversion_breakpoint	SO:0001021
1	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]	SO	186581	SO:0001023	SO:0001023	allele	SO:0001507
1	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]	SO	186582	SO:0001024	SO:0001024	haplotype	SO:0001507
1	"An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]	\N	allele	\N	\N	sequence	"A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]	SO	186583	SO:0001025	SO:0001025	polymorphic_sequence_variant	SO:0001023
1	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	SO	186584	SO:0001026	SO:0001026	genome	SO:0001260
1	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]	SO	186585	SO:0001027	SO:0001027	genotype	SO:0001507
1	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]	SO	186586	SO:0001028	SO:0001028	diplotype	SO:0001507
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	186587	SO:0001029	SO:0001029	direction_attribute	SO:0000733
1	"" []	\N	direction_attribute	\N	\N	sequence	"Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]	SO	186588	SO:0001030	SO:0001030	forward	SO:0001029
1	"" []	\N	direction_attribute	\N	\N	sequence	"Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke]	SO	186589	SO:0001031	SO:0001031	reverse	SO:0001029
1	"" []	\N	mitochondrial_sequence	\N	\N	sequence	"" []	SO	186590	SO:0001032	SO:0001032	mitochondrial_DNA	SO:0000737
1	"" []	\N	chloroplast_sequence	\N	\N	sequence	"" []	SO	186591	SO:0001033	SO:0001033	chloroplast_DNA	SO:0000745
1	"" []	\N	intron_domain	\N	\N	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	186592	SO:0001034	SO:0001034	mirtron	SO:0001014
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	SO	186593	SO:0001035	SO:0001035	piRNA	SO:0000655
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	186594	SO:0001036	SO:0001036	arginyl_tRNA	SO:0000253
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SO	186595	SO:0001037	SO:0001037	mobile_genetic_element	SO:0001411
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SO	186596	SO:0001037	SO:0001037	mobile_genetic_element	SO:0000001
1	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"An MGE that is not integrated into the host chromosome." [SO:ke]	SO	186597	SO:0001038	SO:0001038	extrachromosomal_mobile_genetic_element	SO:0001037
1	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SOFA	mobile_genetic_element	SOFA	SOFA	sequence	"An MGE that is integrated into the host chromosome." [SO:ke]	SO	186598	SO:0001039	SO:0001039	integrated_mobile_genetic_element	SO:0001037
1	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"A plasmid sequence that is integrated within the host chromosome." [SO:ke]	SO	186599	SO:0001040	SO:0001040	integrated_plasmid	SO:0001039
1	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	186600	SO:0001041	SO:0001041	viral_sequence	SO:0001038
1	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	186601	SO:0001041	SO:0001041	viral_sequence	SO:0001235
1	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	186602	SO:0001042	SO:0001042	phage_sequence	SO:0001041
1	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	\N	integration_excision_site	\N	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	186603	SO:0001043	SO:0001043	attCtn_site	SO:0000946
1	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	\N	conjugative_transposon	\N	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	186604	SO:0001043	SO:0001043	attCtn_site	SO:0000371
1	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	\N	non_processed_pseudogene	\N	\N	sequence	"A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]	SO	186605	SO:0001044	SO:0001044	nuclear_mt_pseudogene	SO:0001760
1	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]	SO	186606	SO:0001045	SO:0001045	cointegrated_plasmid	SO:0001039
1	"A region located within an inversion site." [SO:ke]	\N	inversion_site_part	\N	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	186607	SO:0001046	SO:0001046	IRLinv_site	SO:0001048
1	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	\N	inversion_site	\N	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	186608	SO:0001046	SO:0001046	IRLinv_site	SO:0000948
1	"A region located within an inversion site." [SO:ke]	\N	inversion_site_part	\N	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	186609	SO:0001047	SO:0001047	IRRinv_site	SO:0001048
1	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	\N	inversion_site	\N	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	186610	SO:0001047	SO:0001047	IRRinv_site	SO:0000948
1	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"A region located within an inversion site." [SO:ke]	SO	186611	SO:0001048	SO:0001048	inversion_site_part	SO:0000342
1	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	\N	genomic_island	\N	\N	sequence	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	SO	186612	SO:0001049	SO:0001049	defective_conjugative_transposon	SO:0000772
1	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	186613	SO:0001050	SO:0001050	repeat_fragment	SO:0000840
1	"A repeat that is disrupted by the insertion of another element." [SO:ke]	\N	nested_repeat	\N	\N	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	186614	SO:0001050	SO:0001050	repeat_fragment	SO:0001649
1	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	186615	SO:0001054	SO:0001054	transposon_fragment	SO:0000840
1	"A transposon that is disrupted by the insertion of another element." [SO:ke]	\N	nested_transposon	\N	\N	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	186616	SO:0001054	SO:0001054	transposon_fragment	SO:0001648
1	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SO	186617	SO:0001055	SO:0001055	transcriptional_cis_regulatory_region	SO:0001679
1	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A regulatory_region that modulates splicing." [SO:ke]	SO	186618	SO:0001056	SO:0001056	splicing_regulatory_region	SO:0001679
1	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	\N	sequence	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	SO	186619	SO:0001058	SO:0001058	promoter_targeting_sequence	SO:0001055
1	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SO	186620	SO:0001059	SO:0001059	sequence_alteration	SO:0000110
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	186621	SO:0001061	SO:0001061	propeptide_cleavage_site	SO:0100011
1	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	biosapiens	propeptide	biosapiens	biosapiens	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	186622	SO:0001061	SO:0001061	propeptide_cleavage_site	SO:0001062
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	186623	SO:0001062	SO:0001062	propeptide	SO:0100011
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	SO	186624	SO:0001063	SO:0001063	immature_peptide_region	SO:0000839
1	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	biosapiens	mature_protein_region	biosapiens,SOFA	biosapiens	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	186625	SO:0001064	SO:0001064	active_peptide	SO:0000419
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]	SO	186626	SO:0001066	SO:0001066	compositionally_biased_region_of_peptide	SO:0000839
1	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	SO	186627	SO:0001067	SO:0001067	polypeptide_motif	SO:0100021
1	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	SO	186628	SO:0001068	SO:0001068	polypeptide_repeat	SO:0100021
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	SO	186629	SO:0001070	SO:0001070	polypeptide_structural_region	SO:0000839
1	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	SO	186630	SO:0001071	SO:0001071	membrane_structure	SO:0001070
1	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	186631	SO:0001072	SO:0001072	extramembrane_polypeptide_region	SO:0001070
1	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	biosapiens	membrane_structure	biosapiens	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	186632	SO:0001072	SO:0001072	extramembrane_polypeptide_region	SO:0001071
1	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	biosapiens	extramembrane_polypeptide_region	biosapiens	biosapiens	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	186633	SO:0001073	SO:0001073	cytoplasmic_polypeptide_region	SO:0001072
1	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	biosapiens	extramembrane_polypeptide_region	biosapiens	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	186634	SO:0001074	SO:0001074	non_cytoplasmic_polypeptide_region	SO:0001072
1	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	186635	SO:0001075	SO:0001075	intramembrane_polypeptide_region	SO:0001070
1	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	biosapiens	membrane_structure	biosapiens	biosapiens	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	186636	SO:0001075	SO:0001075	intramembrane_polypeptide_region	SO:0001071
1	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	biosapiens	intramembrane_polypeptide_region	biosapiens	biosapiens	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	186637	SO:0001076	SO:0001076	membrane_peptide_loop	SO:0001075
1	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	biosapiens	intramembrane_polypeptide_region	biosapiens	biosapiens	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	186638	SO:0001077	SO:0001077	transmembrane_polypeptide_region	SO:0001075
1	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	SO	186639	SO:0001078	SO:0001078	polypeptide_secondary_structure	SO:0001070
1	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	SO	186640	SO:0001079	SO:0001079	polypeptide_structural_motif	SO:0001070
1	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	biosapiens	polypeptide_structural_motif	biosapiens	biosapiens	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	186641	SO:0001080	SO:0001080	coiled_coil	SO:0001079
1	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	biosapiens	polypeptide_structural_motif	biosapiens	biosapiens	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	186642	SO:0001081	SO:0001081	helix_turn_helix	SO:0001079
1	"A comment about the sequence." [SO:ke]	biosapiens	remark	SOFA	biosapiens	sequence	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	SO	186643	SO:0001082	SO:0001082	polypeptide_sequencing_information	SO:0000700
1	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	biosapiens	polypeptide_sequencing_information	biosapiens	biosapiens	sequence	"Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]	SO	186644	SO:0001083	SO:0001083	non_adjacent_residues	SO:0001082
1	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	biosapiens	polypeptide_sequencing_information	biosapiens	biosapiens	sequence	"The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]	SO	186645	SO:0001084	SO:0001084	non_terminal_residue	SO:0001082
1	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	biosapiens	polypeptide_sequencing_information	biosapiens	biosapiens	sequence	"Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]	SO	186646	SO:0001085	SO:0001085	sequence_conflict	SO:0001082
1	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	biosapiens	polypeptide_sequencing_information	biosapiens	biosapiens	sequence	"Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]	SO	186647	SO:0001086	SO:0001086	sequence_uncertainty	SO:0001082
1	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	186648	SO:0001089	SO:0001089	post_translationally_modified_region	SO:0100001
1	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	186649	SO:0001092	SO:0001092	polypeptide_metal_contact	SO:0001656
1	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	186650	SO:0001092	SO:0001092	polypeptide_metal_contact	SO:0100002
1	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	biosapiens	protein_binding_site	SOFA	biosapiens	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	186651	SO:0001093	SO:0001093	protein_protein_contact	SO:0000410
1	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	186652	SO:0001093	SO:0001093	protein_protein_contact	SO:0100002
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	186653	SO:0001094	SO:0001094	polypeptide_calcium_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	186654	SO:0001095	SO:0001095	polypeptide_cobalt_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	186655	SO:0001096	SO:0001096	polypeptide_copper_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	186656	SO:0001097	SO:0001097	polypeptide_iron_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	186657	SO:0001098	SO:0001098	polypeptide_magnesium_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	186658	SO:0001099	SO:0001099	polypeptide_manganese_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	186659	SO:0001100	SO:0001100	polypeptide_molybdenum_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	186660	SO:0001101	SO:0001101	polypeptide_nickel_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	186661	SO:0001102	SO:0001102	polypeptide_tungsten_ion_contact_site	SO:0001092
1	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	biosapiens	polypeptide_metal_contact	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	186662	SO:0001103	SO:0001103	polypeptide_zinc_ion_contact_site	SO:0001092
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	biosapiens	amino_acid	\N	biosapiens	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	186663	SO:0001104	SO:0001104	catalytic_residue	SO:0001237
1	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	biosapiens	polypeptide_catalytic_motif	biosapiens	biosapiens	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	186664	SO:0001104	SO:0001104	catalytic_residue	SO:0100019
1	"A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]	biosapiens	ligand_binding_site	\N	biosapiens	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	186665	SO:0001105	SO:0001105	polypeptide_ligand_contact	SO:0001657
1	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	186666	SO:0001105	SO:0001105	polypeptide_ligand_contact	SO:0100002
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186667	SO:0001106	SO:0001106	asx_motif	SO:0001078
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186668	SO:0001107	SO:0001107	beta_bulge	SO:0001078
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186669	SO:0001108	SO:0001108	beta_bulge_loop	SO:0001078
1	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_bulge_loop	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186670	SO:0001109	SO:0001109	beta_bulge_loop_five	SO:0001108
1	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_bulge_loop	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186671	SO:0001110	SO:0001110	beta_bulge_loop_six	SO:0001108
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	186672	SO:0001111	SO:0001111	beta_strand	SO:0001078
1	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	beta_strand	biosapiens	biosapiens	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	186673	SO:0001112	SO:0001112	antiparallel_beta_strand	SO:0001111
1	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	beta_strand	biosapiens	biosapiens	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	186674	SO:0001113	SO:0001113	parallel_beta_strand	SO:0001111
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	186675	SO:0001114	SO:0001114	peptide_helix	SO:0001078
1	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	biosapiens	peptide_helix	biosapiens	biosapiens	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	186676	SO:0001115	SO:0001115	left_handed_peptide_helix	SO:0001114
1	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	biosapiens	peptide_helix	biosapiens	biosapiens	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	186677	SO:0001116	SO:0001116	right_handed_peptide_helix	SO:0001114
1	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	biosapiens	right_handed_peptide_helix	biosapiens	biosapiens	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	186678	SO:0001117	SO:0001117	alpha_helix	SO:0001116
1	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	biosapiens	right_handed_peptide_helix	biosapiens	biosapiens	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	186679	SO:0001118	SO:0001118	pi_helix	SO:0001116
1	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	biosapiens	right_handed_peptide_helix	biosapiens	biosapiens	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	186680	SO:0001119	SO:0001119	three_ten_helix	SO:0001116
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186681	SO:0001120	SO:0001120	polypeptide_nest_motif	SO:0001078
1	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	polypeptide_nest_motif	biosapiens	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186682	SO:0001121	SO:0001121	polypeptide_nest_left_right_motif	SO:0001120
1	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	polypeptide_nest_motif	biosapiens	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186683	SO:0001122	SO:0001122	polypeptide_nest_right_left_motif	SO:0001120
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186684	SO:0001123	SO:0001123	schellmann_loop	SO:0001078
1	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	schellmann_loop	biosapiens	biosapiens	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186685	SO:0001124	SO:0001124	schellmann_loop_seven	SO:0001123
1	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	schellmann_loop	biosapiens	biosapiens	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186686	SO:0001125	SO:0001125	schellmann_loop_six	SO:0001123
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186687	SO:0001126	SO:0001126	serine_threonine_motif	SO:0001078
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186688	SO:0001127	SO:0001127	serine_threonine_staple_motif	SO:0001078
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	186689	SO:0001128	SO:0001128	polypeptide_turn_motif	SO:0001078
1	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn	biosapiens	biosapiens	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186690	SO:0001129	SO:0001129	asx_turn_left_handed_type_one	SO:0000912
1	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn	biosapiens	biosapiens	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186691	SO:0001130	SO:0001130	asx_turn_left_handed_type_two	SO:0000912
1	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn	biosapiens	biosapiens	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186692	SO:0001131	SO:0001131	asx_turn_right_handed_type_two	SO:0000912
1	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	asx_turn	biosapiens	biosapiens	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186693	SO:0001132	SO:0001132	asx_turn_right_handed_type_one	SO:0000912
1	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186694	SO:0001133	SO:0001133	beta_turn	SO:0001128
1	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186695	SO:0001134	SO:0001134	beta_turn_left_handed_type_one	SO:0001133
1	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186696	SO:0001135	SO:0001135	beta_turn_left_handed_type_two	SO:0001133
1	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186697	SO:0001136	SO:0001136	beta_turn_right_handed_type_one	SO:0001133
1	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186698	SO:0001137	SO:0001137	beta_turn_right_handed_type_two	SO:0001133
1	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186699	SO:0001138	SO:0001138	gamma_turn	SO:0001128
1	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	gamma_turn	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186700	SO:0001139	SO:0001139	gamma_turn_classic	SO:0001138
1	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	gamma_turn	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186701	SO:0001140	SO:0001140	gamma_turn_inverse	SO:0001138
1	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186702	SO:0001141	SO:0001141	serine_threonine_turn	SO:0001128
1	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	serine_threonine_turn	biosapiens	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186703	SO:0001142	SO:0001142	st_turn_left_handed_type_one	SO:0001141
1	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	serine_threonine_turn	biosapiens	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186704	SO:0001143	SO:0001143	st_turn_left_handed_type_two	SO:0001141
1	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	serine_threonine_turn	biosapiens	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186705	SO:0001144	SO:0001144	st_turn_right_handed_type_one	SO:0001141
1	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	serine_threonine_turn	biosapiens	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	186706	SO:0001145	SO:0001145	st_turn_right_handed_type_two	SO:0001141
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	SO	186707	SO:0001146	SO:0001146	polypeptide_variation_site	SO:0000839
1	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	biosapiens	polypeptide_variation_site	biosapiens	biosapiens	sequence	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	SO	186708	SO:0001147	SO:0001147	natural_variant_site	SO:0001146
1	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	biosapiens	polypeptide_variation_site	biosapiens	biosapiens	sequence	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	SO	186709	SO:0001148	SO:0001148	mutated_variant_site	SO:0001146
1	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	biosapiens	polypeptide_variation_site	biosapiens	biosapiens	sequence	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	SO	186710	SO:0001149	SO:0001149	alternate_sequence_site	SO:0001146
1	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	186711	SO:0001150	SO:0001150	beta_turn_type_six	SO:0001133
1	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	biosapiens	beta_turn_type_six	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	186712	SO:0001151	SO:0001151	beta_turn_type_six_a	SO:0001150
1	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	biosapiens	beta_turn_type_six_a	biosapiens	biosapiens	sequence	"" []	SO	186713	SO:0001152	SO:0001152	beta_turn_type_six_a_one	SO:0001151
1	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	biosapiens	beta_turn_type_six_a	biosapiens	biosapiens	sequence	"" []	SO	186714	SO:0001153	SO:0001153	beta_turn_type_six_a_two	SO:0001151
1	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	biosapiens	beta_turn_type_six	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	186715	SO:0001154	SO:0001154	beta_turn_type_six_b	SO:0001150
1	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	186716	SO:0001155	SO:0001155	beta_turn_type_eight	SO:0001133
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	186717	SO:0001156	SO:0001156	DRE_motif	SO:0000713
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	186718	SO:0001156	SO:0001156	DRE_motif	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	SO	186719	SO:0001157	SO:0001157	DMv4_motif	SO:0001659
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	186720	SO:0001158	SO:0001158	E_box_motif	SO:0000713
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	186721	SO:0001158	SO:0001158	E_box_motif	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	186722	SO:0001159	SO:0001159	DMv5_motif	SO:0001659
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	186723	SO:0001159	SO:0001159	DMv5_motif	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	186724	SO:0001160	SO:0001160	DMv3_motif	SO:0001659
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	186725	SO:0001160	SO:0001160	DMv3_motif	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	186726	SO:0001161	SO:0001161	DMv2_motif	SO:0001659
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	186727	SO:0001161	SO:0001161	DMv2_motif	SO:0000170
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	186728	SO:0001162	SO:0001162	MTE	SO:0001660
1	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	186729	SO:0001162	SO:0001162	MTE	SO:0001669
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	186730	SO:0001163	SO:0001163	INR1_motif	SO:0000713
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	186731	SO:0001163	SO:0001163	INR1_motif	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	186732	SO:0001164	SO:0001164	DPE1_motif	SO:0001659
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	186733	SO:0001164	SO:0001164	DPE1_motif	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	186734	SO:0001165	SO:0001165	DMv1_motif	SO:0001659
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	186735	SO:0001165	SO:0001165	DMv1_motif	SO:0000170
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	186736	SO:0001166	SO:0001166	GAGA_motif	SO:0000713
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	186737	SO:0001166	SO:0001166	GAGA_motif	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	186738	SO:0001167	SO:0001167	NDM2_motif	SO:0001659
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	186739	SO:0001167	SO:0001167	NDM2_motif	SO:0000170
1	"" []	\N	promoter_element	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	186740	SO:0001168	SO:0001168	NDM3_motif	SO:0001659
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	186741	SO:0001168	SO:0001168	NDM3_motif	SO:0000170
1	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	186742	SO:0001169	SO:0001169	ds_RNA_viral_sequence	SO:0001041
1	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	\N	terminal_inverted_repeat_element	\N	\N	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	186743	SO:0001170	SO:0001170	polinton	SO:0000208
1	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	\N	large_subunit_rRNA	SOFA	\N	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	186744	SO:0001171	SO:0001171	rRNA_21S	SO:0000651
1	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"A region of a tRNA." [RSC:cb]	SO	186745	SO:0001172	SO:0001172	tRNA_region	SO:0000834
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A region of a tRNA." [RSC:cb]	SO	186746	SO:0001172	SO:0001172	tRNA_region	SO:0000253
1	"A region of a tRNA." [RSC:cb]	\N	tRNA_region	\N	\N	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	186747	SO:0001173	SO:0001173	anticodon_loop	SO:0001172
1	"A region of a tRNA." [RSC:cb]	\N	tRNA_region	\N	\N	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	186748	SO:0001174	SO:0001174	anticodon	SO:0001172
1	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	\N	anticodon_loop	\N	\N	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	186749	SO:0001174	SO:0001174	anticodon	SO:0001173
1	"A region of a tRNA." [RSC:cb]	\N	tRNA_region	\N	\N	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	186750	SO:0001175	SO:0001175	CCA_tail	SO:0001172
1	"A region of a tRNA." [RSC:cb]	\N	tRNA_region	\N	\N	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	186751	SO:0001176	SO:0001176	DHU_loop	SO:0001172
1	"A region of a tRNA." [RSC:cb]	\N	tRNA_region	\N	\N	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	186752	SO:0001177	SO:0001177	T_loop	SO:0001172
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	186753	SO:0001178	SO:0001178	pyrrolysine_tRNA_primary_transcript	SO:0000210
1	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	\N	C_D_box_snoRNA	SOFA	\N	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	186754	SO:0001179	SO:0001179	U3_snoRNA	SO:0000593
1	"A region of UTR." [SO:ke]	\N	UTR_region	SOFA	\N	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	186755	SO:0001180	SO:0001180	AU_rich_element	SO:0000837
1	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	three_prime_UTR	SOFA	\N	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	186756	SO:0001180	SO:0001180	AU_rich_element	SO:0000205
1	"A region of UTR." [SO:ke]	\N	UTR_region	SOFA	\N	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	186757	SO:0001181	SO:0001181	Bruno_response_element	SO:0000837
1	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	three_prime_UTR	SOFA	\N	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	186758	SO:0001181	SO:0001181	Bruno_response_element	SO:0000205
1	"A region of UTR." [SO:ke]	\N	UTR_region	SOFA	\N	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	186759	SO:0001182	SO:0001182	iron_responsive_element	SO:0000837
1	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	\N	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	186760	SO:0001182	SO:0001182	iron_responsive_element	SO:0000203
1	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]	SO	186761	SO:0001183	SO:0001183	morpholino_backbone	SO:0000348
1	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]	SO	186762	SO:0001184	SO:0001184	PNA	SO:0000348
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	186763	SO:0001185	SO:0001185	enzymatic	SO:0000733
1	"An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	\N	enzymatic	\N	\N	sequence	"An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]	SO	186764	SO:0001186	SO:0001186	ribozymic	SO:0001185
1	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	\N	H_ACA_box_snoRNA	\N	\N	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	186765	SO:0001187	SO:0001187	pseudouridylation_guide_snoRNA	SO:0000594
1	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]	SO	186766	SO:0001188	SO:0001188	LNA	SO:0000348
1	"An oligo composed of synthetic nucleotides." [SO:ke]	\N	synthetic_oligo	\N	\N	sequence	"An oligo composed of LNA residues." [RSC:cb]	SO	186767	SO:0001189	SO:0001189	LNA_oligo	SO:0001247
1	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]	SO	186768	SO:0001190	SO:0001190	TNA	SO:0000348
1	"An oligo composed of synthetic nucleotides." [SO:ke]	\N	synthetic_oligo	\N	\N	sequence	"An oligo composed of TNA residues." [RSC:cb]	SO	186769	SO:0001191	SO:0001191	TNA_oligo	SO:0001247
1	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]	SO	186770	SO:0001192	SO:0001192	GNA	SO:0000348
1	"An oligo composed of synthetic nucleotides." [SO:ke]	\N	synthetic_oligo	\N	\N	sequence	"An oligo composed of GNA residues." [RSC:cb]	SO	186771	SO:0001193	SO:0001193	GNA_oligo	SO:0001247
1	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]	\N	GNA	\N	\N	sequence	"An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]	SO	186772	SO:0001194	SO:0001194	R_GNA	SO:0001192
1	"An oligo composed of GNA residues." [RSC:cb]	\N	GNA_oligo	\N	\N	sequence	"An oligo composed of (R)-GNA residues." [RSC:cb]	SO	186773	SO:0001195	SO:0001195	R_GNA_oligo	SO:0001193
1	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]	\N	GNA	\N	\N	sequence	"An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]	SO	186774	SO:0001196	SO:0001196	S_GNA	SO:0001192
1	"An oligo composed of GNA residues." [RSC:cb]	\N	GNA_oligo	\N	\N	sequence	"An oligo composed of (S)-GNA residues." [RSC:cb]	SO	186775	SO:0001197	SO:0001197	S_GNA_oligo	SO:0001193
1	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	186776	SO:0001198	SO:0001198	ds_DNA_viral_sequence	SO:0001041
1	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	186777	SO:0001199	SO:0001199	ss_RNA_viral_sequence	SO:0001041
1	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	\N	ss_RNA_viral_sequence	\N	\N	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	186778	SO:0001200	SO:0001200	negative_sense_ssRNA_viral_sequence	SO:0001199
1	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	\N	ss_RNA_viral_sequence	\N	\N	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	186779	SO:0001201	SO:0001201	positive_sense_ssRNA_viral_sequence	SO:0001199
1	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	\N	ss_RNA_viral_sequence	\N	\N	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	186780	SO:0001202	SO:0001202	ambisense_ssRNA_viral_sequence	SO:0001199
1	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	186781	SO:0001203	SO:0001203	RNA_polymerase_promoter	SO:0000167
1	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	186782	SO:0001204	SO:0001204	Phage_RNA_Polymerase_Promoter	SO:0001203
1	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	Phage_RNA_Polymerase_Promoter	\N	\N	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	186783	SO:0001205	SO:0001205	SP6_RNA_Polymerase_Promoter	SO:0001204
1	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	Phage_RNA_Polymerase_Promoter	\N	\N	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	186784	SO:0001206	SO:0001206	T3_RNA_Polymerase_Promoter	SO:0001204
1	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	Phage_RNA_Polymerase_Promoter	\N	\N	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	186785	SO:0001207	SO:0001207	T7_RNA_Polymerase_Promoter	SO:0001204
1	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	\N	EST	SOFA	\N	sequence	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	186786	SO:0001208	SO:0001208	five_prime_EST	SO:0000345
1	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	\N	EST	SOFA	\N	sequence	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	186787	SO:0001209	SO:0001209	three_prime_EST	SO:0000345
1	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	186788	SO:0001210	SO:0001210	translational_frameshift	SO:0000836
1	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	\N	translational_frameshift	\N	\N	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	186789	SO:0001211	SO:0001211	plus_1_translational_frameshift	SO:0001210
1	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	\N	translational_frameshift	\N	\N	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	186790	SO:0001212	SO:0001212	plus_2_translational_frameshift	SO:0001210
1	"A self spliced intron." [SO:ke]	\N	autocatalytically_spliced_intron	SOFA	\N	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	186791	SO:0001213	SO:0001213	group_III_intron	SO:0000588
1	"A region of an exon." [RSC:cb]	SOFA	exon_region	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	186792	SO:0001214	SO:0001214	noncoding_region_of_exon	SO:0000852
1	"A region of an exon." [RSC:cb]	SOFA	exon_region	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	186793	SO:0001215	SO:0001215	coding_region_of_exon	SO:0000852
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	186794	SO:0001216	SO:0001216	endonuclease_spliced_intron	SO:0000188
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	186795	SO:0001217	SO:0001217	protein_coding_gene	SO:0000704
1	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	\N	insertion	DBVAR,SOFA	\N	sequence	"An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]	SO	186796	SO:0001218	SO:0001218	transgenic_insertion	SO:0000667
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	186797	SO:0001219	SO:0001219	retrogene	SO:0000704
1	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	\N	silenced	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	SO	186798	SO:0001220	SO:0001220	silenced_by_RNA_interference	SO:0000893
1	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	\N	silenced	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	SO	186799	SO:0001221	SO:0001221	silenced_by_histone_modification	SO:0000893
1	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	\N	silenced_by_histone_modification	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	186800	SO:0001222	SO:0001222	silenced_by_histone_methylation	SO:0001221
1	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	\N	silenced_by_histone_modification	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	186801	SO:0001223	SO:0001223	silenced_by_histone_deacetylation	SO:0001221
1	"A gene that is silenced." [SO:xp]	\N	silenced_gene	\N	\N	sequence	"A gene that is silenced by RNA interference." [SO:xp]	SO	186802	SO:0001224	SO:0001224	gene_silenced_by_RNA_interference	SO:0000127
1	"A gene that is silenced." [SO:xp]	\N	silenced_gene	\N	\N	sequence	"A gene that is silenced by histone modification." [SO:xp]	SO	186803	SO:0001225	SO:0001225	gene_silenced_by_histone_modification	SO:0000127
1	"A gene that is silenced by histone modification." [SO:xp]	\N	gene_silenced_by_histone_modification	\N	\N	sequence	"A gene that is silenced by histone methylation." [SO:xp]	SO	186804	SO:0001226	SO:0001226	gene_silenced_by_histone_methylation	SO:0001225
1	"A gene that is silenced by histone modification." [SO:xp]	\N	gene_silenced_by_histone_modification	\N	\N	sequence	"A gene that is silenced by histone deacetylation." [SO:xp]	SO	186805	SO:0001227	SO:0001227	gene_silenced_by_histone_deacetylation	SO:0001225
1	"" []	\N	modified_uridine	\N	\N	sequence	"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]	SO	186806	SO:0001228	SO:0001228	dihydrouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]	SO	186807	SO:0001229	SO:0001229	pseudouridine	SO:0001277
1	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	SO	186808	SO:0001230	SO:0001230	inosine	SO:0000250
1	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]	SO	186809	SO:0001231	SO:0001231	seven_methylguanine	SO:0000250
1	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]	SO	186810	SO:0001232	SO:0001232	ribothymidine	SO:0000250
1	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	\N	modified_inosine	\N	\N	sequence	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	SO	186811	SO:0001233	SO:0001233	methylinosine	SO:0001274
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb]	SO	186812	SO:0001234	SO:0001234	mobile	SO:0000733
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SO	186813	SO:0001235	SO:0001235	replicon	SO:0001411
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SO	186814	SO:0001236	SO:0001236	base	SO:0001411
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	SO	186815	SO:0001237	SO:0001237	amino_acid	SO:0001411
1	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	SO	186816	SO:0001237	SO:0001237	amino_acid	SO:0000104
1	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	\N	TSS	SOFA	\N	sequence	"" []	SO	186817	SO:0001238	SO:0001238	major_TSS	SO:0000315
1	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	\N	TSS	SOFA	\N	sequence	"" []	SO	186818	SO:0001239	SO:0001239	minor_TSS	SO:0000315
1	"" []	\N	gene_component_region	SOFA	\N	sequence	"The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]	SO	186819	SO:0001240	SO:0001240	TSS_region	SO:0000842
1	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	186820	SO:0001241	SO:0001241	encodes_alternate_transcription_start_sites	SO:0000401
1	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	186821	SO:0001243	SO:0001243	miRNA_primary_transcript_region	SO:0000835
1	"A part of an miRNA primary_transcript." [SO:ke]	\N	miRNA_primary_transcript_region	\N	\N	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	186822	SO:0001244	SO:0001244	pre_miRNA	SO:0001243
1	"A primary transcript encoding a micro RNA." [SO:ke]	\N	miRNA_primary_transcript	\N	\N	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	186823	SO:0001244	SO:0001244	pre_miRNA	SO:0000647
1	"A part of an miRNA primary_transcript." [SO:ke]	\N	miRNA_primary_transcript_region	\N	\N	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	186824	SO:0001245	SO:0001245	miRNA_stem	SO:0001243
1	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	\N	pre_miRNA	\N	\N	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	186825	SO:0001245	SO:0001245	miRNA_stem	SO:0001244
1	"A part of an miRNA primary_transcript." [SO:ke]	\N	miRNA_primary_transcript_region	\N	\N	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	186826	SO:0001246	SO:0001246	miRNA_loop	SO:0001243
1	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	\N	pre_miRNA	\N	\N	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	186827	SO:0001246	SO:0001246	miRNA_loop	SO:0001244
1	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"An oligo composed of synthetic nucleotides." [SO:ke]	SO	186828	SO:0001247	SO:0001247	synthetic_oligo	SO:0000696
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SO	186829	SO:0001248	SO:0001248	assembly	SO:0001410
1	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	\N	sequence	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	SO	186830	SO:0001249	SO:0001249	fragment_assembly	SO:0001248
1	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	\N	fragment_assembly	\N	\N	sequence	"A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]	SO	186831	SO:0001250	SO:0001250	fingerprint_map	SO:0001249
1	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	\N	fragment_assembly	\N	\N	sequence	"An STS map is a physical map organized by the unique STS landmarks." [SO:ke]	SO	186832	SO:0001251	SO:0001251	STS_map	SO:0001249
1	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	\N	fragment_assembly	\N	\N	sequence	"A radiation hybrid map is a physical map." [SO:ke]	SO	186833	SO:0001252	SO:0001252	RH_map	SO:0001249
1	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	\N	sequence	"A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]	SO	186834	SO:0001253	SO:0001253	sonicate_fragment	SO:0000143
1	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	chromosome_number_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	186835	SO:0001254	SO:0001254	polyploid	SO:1000182
1	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	\N	polyploid	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	186836	SO:0001255	SO:0001255	autopolyploid	SO:0001254
1	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	\N	polyploid	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	186837	SO:0001256	SO:0001256	allopolyploid	SO:0001254
1	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	\N	nuclease_binding_site	SOFA	\N	sequence	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	SO	186838	SO:0001257	SO:0001257	homing_endonuclease_binding_site	SO:0000059
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	186839	SO:0001258	SO:0001258	octamer_motif	SO:0000713
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	186840	SO:0001258	SO:0001258	octamer_motif	SO:0000170
1	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"A chromosome originating in an apicoplast." [SO:xp]	SO	186841	SO:0001259	SO:0001259	apicoplast_chromosome	SO:0000340
1	"A region of sequence implicated in an experimental result." [SO:ke]	\N	experimental_result_region	SOFA	\N	sequence	"A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]	SO	186842	SO:0001261	SO:0001261	overlapping_feature_set	SO:0000703
1	"A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]	\N	overlapping_feature_set	\N	\N	sequence	"A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]	SO	186843	SO:0001262	SO:0001262	overlapping_EST_set	SO:0001261
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	186844	SO:0001263	SO:0001263	ncRNA_gene	SO:0000704
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186845	SO:0001264	SO:0001264	gRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186846	SO:0001265	SO:0001265	miRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186847	SO:0001266	SO:0001266	scRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186848	SO:0001267	SO:0001267	snoRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186849	SO:0001268	SO:0001268	snRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186850	SO:0001269	SO:0001269	SRP_RNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186851	SO:0001270	SO:0001270	stRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186852	SO:0001271	SO:0001271	tmRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"" []	SO	186853	SO:0001272	SO:0001272	tRNA_gene	SO:0001263
1	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	SO	186854	SO:0001273	SO:0001273	modified_adenosine	SO:0000250
1	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	\N	inosine	\N	\N	sequence	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	SO	186855	SO:0001274	SO:0001274	modified_inosine	SO:0001230
1	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	SO	186856	SO:0001275	SO:0001275	modified_cytidine	SO:0000250
1	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"" []	SO	186857	SO:0001276	SO:0001276	modified_guanosine	SO:0000250
1	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"" []	SO	186858	SO:0001277	SO:0001277	modified_uridine	SO:0000250
1	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	\N	modified_inosine	\N	\N	sequence	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	186859	SO:0001278	SO:0001278	one_methylinosine	SO:0001274
1	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	\N	modified_inosine	\N	\N	sequence	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	186860	SO:0001279	SO:0001279	one_two_prime_O_dimethylinosine	SO:0001274
1	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	\N	modified_inosine	\N	\N	sequence	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	186861	SO:0001280	SO:0001280	two_prime_O_methylinosine	SO:0001274
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186862	SO:0001281	SO:0001281	three_methylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186863	SO:0001282	SO:0001282	five_methylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186864	SO:0001283	SO:0001283	two_prime_O_methylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186865	SO:0001284	SO:0001284	two_thiocytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186866	SO:0001285	SO:0001285	N4_acetylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186867	SO:0001286	SO:0001286	five_formylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186868	SO:0001287	SO:0001287	five_two_prime_O_dimethylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186869	SO:0001288	SO:0001288	N4_acetyl_2_prime_O_methylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186870	SO:0001289	SO:0001289	lysidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186871	SO:0001290	SO:0001290	N4_methylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186872	SO:0001291	SO:0001291	N4_2_prime_O_dimethylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186873	SO:0001292	SO:0001292	five_hydroxymethylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186874	SO:0001293	SO:0001293	five_formyl_two_prime_O_methylcytidine	SO:0001275
1	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	\N	modified_cytidine	\N	\N	sequence	"N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	186875	SO:0001294	SO:0001294	N4_N4_2_prime_O_trimethylcytidine	SO:0001275
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186876	SO:0001295	SO:0001295	one_methyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186877	SO:0001296	SO:0001296	two_methyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186878	SO:0001297	SO:0001297	N6_methyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186879	SO:0001298	SO:0001298	two_prime_O_methyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186880	SO:0001299	SO:0001299	two_methylthio_N6_methyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186881	SO:0001300	SO:0001300	N6_isopentenyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186882	SO:0001301	SO:0001301	two_methylthio_N6_isopentenyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186883	SO:0001302	SO:0001302	N6_cis_hydroxyisopentenyl_adenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186884	SO:0001303	SO:0001303	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186885	SO:0001304	SO:0001304	N6_glycinylcarbamoyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186886	SO:0001305	SO:0001305	N6_threonylcarbamoyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186887	SO:0001306	SO:0001306	two_methylthio_N6_threonyl_carbamoyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186888	SO:0001307	SO:0001307	N6_methyl_N6_threonylcarbamoyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186889	SO:0001308	SO:0001308	N6_hydroxynorvalylcarbamoyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186890	SO:0001309	SO:0001309	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186891	SO:0001310	SO:0001310	two_prime_O_ribosyladenosine_phosphate	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186892	SO:0001311	SO:0001311	N6_N6_dimethyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186893	SO:0001312	SO:0001312	N6_2_prime_O_dimethyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186894	SO:0001313	SO:0001313	N6_N6_2_prime_O_trimethyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186895	SO:0001314	SO:0001314	one_two_prime_O_dimethyladenosine	SO:0001273
1	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	\N	modified_adenosine	\N	\N	sequence	"N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	186896	SO:0001315	SO:0001315	N6_acetyladenosine	SO:0001273
1	"" []	\N	modified_guanosine	\N	\N	sequence	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	SO	186897	SO:0001316	SO:0001316	seven_deazaguanosine	SO:0001276
1	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_deazaguanosine	\N	\N	sequence	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	186898	SO:0001317	SO:0001317	queuosine	SO:0001316
1	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_deazaguanosine	\N	\N	sequence	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	186899	SO:0001318	SO:0001318	epoxyqueuosine	SO:0001316
1	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_deazaguanosine	\N	\N	sequence	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	186900	SO:0001319	SO:0001319	galactosyl_queuosine	SO:0001316
1	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_deazaguanosine	\N	\N	sequence	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	186901	SO:0001320	SO:0001320	mannosyl_queuosine	SO:0001316
1	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_deazaguanosine	\N	\N	sequence	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	186902	SO:0001321	SO:0001321	seven_cyano_seven_deazaguanosine	SO:0001316
1	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_deazaguanosine	\N	\N	sequence	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	186903	SO:0001322	SO:0001322	seven_aminomethyl_seven_deazaguanosine	SO:0001316
1	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	\N	seven_deazaguanosine	\N	\N	sequence	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	186904	SO:0001323	SO:0001323	archaeosine	SO:0001316
1	"" []	\N	modified_guanosine	\N	\N	sequence	"1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186905	SO:0001324	SO:0001324	one_methylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186906	SO:0001325	SO:0001325	N2_methylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186907	SO:0001326	SO:0001326	seven_methylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186908	SO:0001327	SO:0001327	two_prime_O_methylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186909	SO:0001328	SO:0001328	N2_N2_dimethylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186910	SO:0001329	SO:0001329	N2_2_prime_O_dimethylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186911	SO:0001330	SO:0001330	N2_N2_2_prime_O_trimethylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186912	SO:0001331	SO:0001331	two_prime_O_ribosylguanosine_phosphate	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186913	SO:0001332	SO:0001332	wybutosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186914	SO:0001333	SO:0001333	peroxywybutosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186915	SO:0001334	SO:0001334	hydroxywybutosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186916	SO:0001335	SO:0001335	undermodified_hydroxywybutosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186917	SO:0001336	SO:0001336	wyosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186918	SO:0001337	SO:0001337	methylwyosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186919	SO:0001338	SO:0001338	N2_7_dimethylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186920	SO:0001339	SO:0001339	N2_N2_7_trimethylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186921	SO:0001340	SO:0001340	one_two_prime_O_dimethylguanosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186922	SO:0001341	SO:0001341	four_demethylwyosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186923	SO:0001342	SO:0001342	isowyosine	SO:0001276
1	"" []	\N	modified_guanosine	\N	\N	sequence	"N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186924	SO:0001343	SO:0001343	N2_7_2prirme_O_trimethylguanosine	SO:0001276
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186925	SO:0001344	SO:0001344	five_methyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186926	SO:0001345	SO:0001345	two_prime_O_methyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186927	SO:0001346	SO:0001346	five_two_prime_O_dimethyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186928	SO:0001347	SO:0001347	one_methylpseudouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186929	SO:0001348	SO:0001348	two_prime_O_methylpseudouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186930	SO:0001349	SO:0001349	two_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186931	SO:0001350	SO:0001350	four_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186932	SO:0001351	SO:0001351	five_methyl_2_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186933	SO:0001352	SO:0001352	two_thio_two_prime_O_methyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186934	SO:0001353	SO:0001353	three_three_amino_three_carboxypropyl_uridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186935	SO:0001354	SO:0001354	five_hydroxyuridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186936	SO:0001355	SO:0001355	five_methoxyuridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186937	SO:0001356	SO:0001356	uridine_five_oxyacetic_acid	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186938	SO:0001357	SO:0001357	uridine_five_oxyacetic_acid_methyl_ester	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186939	SO:0001358	SO:0001358	five_carboxyhydroxymethyl_uridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186940	SO:0001359	SO:0001359	five_carboxyhydroxymethyl_uridine_methyl_ester	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186941	SO:0001360	SO:0001360	five_methoxycarbonylmethyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186942	SO:0001361	SO:0001361	five_methoxycarbonylmethyl_two_prime_O_methyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186943	SO:0001362	SO:0001362	five_methoxycarbonylmethyl_two_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186944	SO:0001363	SO:0001363	five_aminomethyl_two_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186945	SO:0001364	SO:0001364	five_methylaminomethyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186946	SO:0001365	SO:0001365	five_methylaminomethyl_two_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186947	SO:0001366	SO:0001366	five_methylaminomethyl_two_selenouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186948	SO:0001367	SO:0001367	five_carbamoylmethyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186949	SO:0001368	SO:0001368	five_carbamoylmethyl_two_prime_O_methyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186950	SO:0001369	SO:0001369	five_carboxymethylaminomethyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186951	SO:0001370	SO:0001370	five_carboxymethylaminomethyl_two_prime_O_methyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186952	SO:0001371	SO:0001371	five_carboxymethylaminomethyl_two_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186953	SO:0001372	SO:0001372	three_methyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186954	SO:0001373	SO:0001373	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186955	SO:0001374	SO:0001374	five_carboxymethyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186956	SO:0001375	SO:0001375	three_two_prime_O_dimethyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186957	SO:0001376	SO:0001376	five_methyldihydrouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186958	SO:0001377	SO:0001377	three_methylpseudouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186959	SO:0001378	SO:0001378	five_taurinomethyluridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186960	SO:0001379	SO:0001379	five_taurinomethyl_two_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186961	SO:0001380	SO:0001380	five_isopentenylaminomethyl_uridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186962	SO:0001381	SO:0001381	five_isopentenylaminomethyl_two_thiouridine	SO:0001277
1	"" []	\N	modified_uridine	\N	\N	sequence	"5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	186963	SO:0001382	SO:0001382	five_isopentenylaminomethyl_two_prime_O_methyluridine	SO:0001277
1	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	nucleotide_to_protein_binding_site	SOFA	\N	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]	SO	186964	SO:0001383	SO:0001383	histone_binding_site	SO:0001654
1	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"" []	SO	186965	SO:0001384	SO:0001384	CDS_fragment	SO:0000316
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified amino acid feature." [SO:ke]	SO	186966	SO:0001385	SO:0001385	modified_amino_acid_feature	SO:0001237
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified glycine amino acid feature." [SO:ke]	SO	186967	SO:0001386	SO:0001386	modified_glycine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified alanine amino acid feature." [SO:ke]	SO	186968	SO:0001387	SO:0001387	modified_L_alanine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified asparagine amino acid feature." [SO:ke]	SO	186969	SO:0001388	SO:0001388	modified_L_asparagine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	SO	186970	SO:0001389	SO:0001389	modified_L_aspartic_acid	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified cysteine amino acid feature." [SO:ke]	SO	186971	SO:0001390	SO:0001390	modified_L_cysteine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"" []	SO	186972	SO:0001391	SO:0001391	modified_L_glutamic_acid	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified threonine amino acid feature." [SO:ke]	SO	186973	SO:0001392	SO:0001392	modified_L_threonine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified tryptophan amino acid feature." [SO:ke]	SO	186974	SO:0001393	SO:0001393	modified_L_tryptophan	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified glutamine amino acid feature." [SO:ke]	SO	186975	SO:0001394	SO:0001394	modified_L_glutamine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified methionine amino acid feature." [SO:ke]	SO	186976	SO:0001395	SO:0001395	modified_L_methionine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified isoleucine amino acid feature." [SO:ke]	SO	186977	SO:0001396	SO:0001396	modified_L_isoleucine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	SO	186978	SO:0001397	SO:0001397	modified_L_phenylalanine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified histidine amino acid feature." [SO:ke]	SO	186979	SO:0001398	SO:0001398	modified_L_histidine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified serine amino acid feature." [SO:ke]	SO	186980	SO:0001399	SO:0001399	modified_L_serine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified lysine amino acid feature." [SO:ke]	SO	186981	SO:0001400	SO:0001400	modified_L_lysine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified leucine amino acid feature." [SO:ke]	SO	186982	SO:0001401	SO:0001401	modified_L_leucine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	SO	186983	SO:0001402	SO:0001402	modified_L_selenocysteine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified valine amino acid feature." [SO:ke]	SO	186984	SO:0001403	SO:0001403	modified_L_valine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified proline amino acid feature." [SO:ke]	SO	186985	SO:0001404	SO:0001404	modified_L_proline	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified tyrosine amino acid feature." [SO:ke]	SO	186986	SO:0001405	SO:0001405	modified_L_tyrosine	SO:0001385
1	"A post translationally modified amino acid feature." [SO:ke]	\N	modified_amino_acid_feature	\N	\N	sequence	"A post translationally modified arginine amino acid feature." [SO:ke]	SO	186987	SO:0001406	SO:0001406	modified_L_arginine	SO:0001385
1	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke]	SO	186988	SO:0001407	SO:0001407	peptidyl	SO:0000443
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	\N	cleaved_peptide_region	biosapiens,SOFA	\N	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	186989	SO:0001408	SO:0001408	cleaved_for_gpi_anchor_region	SO:0100011
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region which is intended for use in an experiment." [SO:cb]	SO	186990	SO:0001409	SO:0001409	biomaterial_region	SO:0000001
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SO	186991	SO:0001410	SO:0001410	experimental_feature	SO:0000001
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SO	186992	SO:0001411	SO:0001411	biological_region	SO:0000001
1	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	SO	186993	SO:0001412	SO:0001412	topologically_defined_region	SO:0000001
1	"" []	\N	chromosome_breakpoint	\N	\N	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	186994	SO:0001413	SO:0001413	translocation_breakpoint	SO:0001021
1	"" []	\N	chromosome_breakpoint	\N	\N	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	186995	SO:0001414	SO:0001414	insertion_breakpoint	SO:0001021
1	"" []	\N	chromosome_breakpoint	\N	\N	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	186996	SO:0001415	SO:0001415	deletion_breakpoint	SO:0001021
1	"The sequences extending on either side of a specific region." [SO:ke]	\N	flanking_region	SOFA	\N	sequence	"A flanking region located five prime of a specific region." [SO:chado]	SO	186997	SO:0001416	SO:0001416	five_prime_flanking_region	SO:0000239
1	"The sequences extending on either side of a specific region." [SO:ke]	\N	flanking_region	SOFA	\N	sequence	"A flanking region located three prime of a specific region." [SO:chado]	SO	186998	SO:0001417	SO:0001417	three_prime_flanking_region	SO:0000239
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]	SO	186999	SO:0001418	SO:0001418	transcribed_fragment	SO:0001410
1	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SOFA	splice_site	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	187000	SO:0001419	SO:0001419	cis_splice_site	SO:0000162
1	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SOFA	splice_site	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	187001	SO:0001420	SO:0001420	trans_splice_site	SO:0000162
1	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"The boundary between an intron and an exon." [SO:ke]	SO	187002	SO:0001421	SO:0001421	splice_junction	SO:0000699
1	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	\N	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	187003	SO:0001422	SO:0001422	conformational_switch	SO:0100001
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	187004	SO:0001423	SO:0001423	dye_terminator_read	SO:0000150
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	187005	SO:0001424	SO:0001424	pyrosequenced_read	SO:0000150
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	187006	SO:0001425	SO:0001425	ligation_based_read	SO:0000150
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	187007	SO:0001426	SO:0001426	polymerase_synthesis_read	SO:0000150
1	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	\N	sequence	"A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]	SO	187008	SO:0001427	SO:0001427	cis_regulatory_frameshift_element	SO:0001679
1	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A sequence assembly derived from expressed sequences." [SO:ke]	SO	187009	SO:0001428	SO:0001428	expressed_sequence_assembly	SO:0000353
1	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	\N	nucleotide_binding_site	\N	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	SO	187010	SO:0001429	SO:0001429	DNA_binding_site	SO:0001655
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]	SO	187011	SO:0001431	SO:0001431	cryptic_gene	SO:0000704
1	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	\N	cDNA_clone	\N	\N	sequence	"A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]	SO	187012	SO:0001433	SO:0001433	three_prime_RACE_clone	SO:0000317
1	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	\N	non_processed_pseudogene	\N	\N	sequence	"A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]	SO	187013	SO:0001434	SO:0001434	cassette_pseudogene	SO:0001760
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187014	SO:0001435	SO:0001435	alanine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187015	SO:0001436	SO:0001436	valine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187016	SO:0001437	SO:0001437	leucine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187017	SO:0001438	SO:0001438	isoleucine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187018	SO:0001439	SO:0001439	proline	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187019	SO:0001440	SO:0001440	tryptophan	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187020	SO:0001441	SO:0001441	phenylalanine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187021	SO:0001442	SO:0001442	methionine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187022	SO:0001443	SO:0001443	glycine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187023	SO:0001444	SO:0001444	serine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187024	SO:0001445	SO:0001445	threonine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187025	SO:0001446	SO:0001446	tyrosine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187026	SO:0001447	SO:0001447	cysteine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187027	SO:0001448	SO:0001448	glutamine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187028	SO:0001449	SO:0001449	asparagine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187029	SO:0001450	SO:0001450	lysine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187030	SO:0001451	SO:0001451	arginine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187031	SO:0001452	SO:0001452	histidine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187032	SO:0001453	SO:0001453	aspartic_acid	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187033	SO:0001454	SO:0001454	glutamic_acid	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187034	SO:0001455	SO:0001455	selenocysteine	SO:0001237
1	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	187035	SO:0001456	SO:0001456	pyrrolysine	SO:0001237
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]	SO	187036	SO:0001457	SO:0001457	transcribed_cluster	SO:0001410
1	"A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]	\N	transcribed_cluster	\N	\N	sequence	"A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]	SO	187037	SO:0001458	SO:0001458	unigene_cluster	SO:0001457
1	"A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]	\N	direct_repeat	SOFA	\N	sequence	"Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]	SO	187038	SO:0001459	SO:0001459	CRISPR	SO:0000314
1	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	nucleotide_to_protein_binding_site	SOFA	\N	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	187039	SO:0001460	SO:0001460	insulator_binding_site	SO:0001654
1	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	\N	insulator	SOFA	\N	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	187040	SO:0001460	SO:0001460	insulator_binding_site	SO:0000627
1	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	nucleotide_to_protein_binding_site	SOFA	\N	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	187041	SO:0001461	SO:0001461	enhancer_binding_site	SO:0001654
1	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	enhancer	SOFA	\N	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	187042	SO:0001461	SO:0001461	enhancer_binding_site	SO:0000165
1	"Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]	\N	sequence_conflict	biosapiens	\N	sequence	"A collection of contigs." [SO:ke]	SO	187043	SO:0001462	SO:0001462	contig_collection	SO:0001085
1	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A collection of contigs." [SO:ke]	SO	187044	SO:0001462	SO:0001462	contig_collection	SO:0001260
1	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	\N	lnc_RNA	\N	\N	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	187045	SO:0001463	SO:0001463	lincRNA	SO:0001877
1	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	\N	EST	SOFA	\N	sequence	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	SO	187046	SO:0001464	SO:0001464	UST	SO:0000345
1	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	\N	UST	\N	\N	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	187047	SO:0001465	SO:0001465	three_prime_UST	SO:0001464
1	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	\N	UST	\N	\N	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	187048	SO:0001466	SO:0001466	five_prime_UST	SO:0001464
1	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	\N	EST	SOFA	\N	sequence	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	187049	SO:0001467	SO:0001467	RST	SO:0000345
1	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	\N	RST	\N	\N	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	187050	SO:0001468	SO:0001468	three_prime_RST	SO:0001467
1	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	\N	RST	\N	\N	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	187051	SO:0001469	SO:0001469	five_prime_RST	SO:0001467
1	"A match to an EST or cDNA sequence." [SO:ke]	\N	expressed_sequence_match	SOFA	\N	sequence	"A match against an UST sequence." [SO:nlw]	SO	187052	SO:0001470	SO:0001470	UST_match	SO:0000102
1	"A match to an EST or cDNA sequence." [SO:ke]	\N	expressed_sequence_match	SOFA	\N	sequence	"A match against an RST sequence." [SO:nlw]	SO	187053	SO:0001471	SO:0001471	RST_match	SO:0000102
1	"A match against a nucleotide sequence." [SO:ke]	\N	nucleotide_match	SOFA	\N	sequence	"A nucleotide match to a primer sequence." [SO:nlw]	SO	187054	SO:0001472	SO:0001472	primer_match	SO:0000347
1	"A part of an miRNA primary_transcript." [SO:ke]	\N	miRNA_primary_transcript_region	\N	\N	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	187055	SO:0001473	SO:0001473	miRNA_antiguide	SO:0001243
1	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"The boundary between the spliced leader and the first exon of the mRNA." [SO:ke]	SO	187056	SO:0001474	SO:0001474	trans_splice_junction	SO:0000699
1	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	187057	SO:0001475	SO:0001475	outron	SO:0000835
1	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	187058	SO:0001476	SO:0001476	natural_plasmid	SO:0000155
1	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	187059	SO:0001476	SO:0001476	natural_plasmid	SO:0001038
1	"A plasmid that is engineered." [SO:xp]	\N	engineered_plasmid	\N	\N	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	187060	SO:0001477	SO:0001477	gene_trap_construct	SO:0000637
1	"A plasmid that is engineered." [SO:xp]	\N	engineered_plasmid	\N	\N	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	187061	SO:0001478	SO:0001478	promoter_trap_construct	SO:0000637
1	"A plasmid that is engineered." [SO:xp]	\N	engineered_plasmid	\N	\N	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	187062	SO:0001479	SO:0001479	enhancer_trap_construct	SO:0000637
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	187063	SO:0001480	SO:0001480	PAC_end	SO:0000150
1	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	\N	PAC	\N	\N	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	187064	SO:0001480	SO:0001480	PAC_end	SO:0000154
1	"A region amplified by a PCR reaction." [SO:ke]	\N	PCR_product	SOFA	\N	sequence	"RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]	SO	187065	SO:0001481	SO:0001481	RAPD	SO:0000006
1	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	enhancer	SOFA	\N	sequence	"" []	SO	187066	SO:0001482	SO:0001482	shadow_enhancer	SO:0000165
1	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SOFA	substitution	SOFA	SOFA	sequence	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SO	187067	SO:0001483	SO:0001483	SNV	SO:1000002
1	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	187068	SO:0001484	SO:0001484	X_element_combinatorial_repeat	SO:0000657
1	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	\N	telomere	SOFA	\N	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	187069	SO:0001484	SO:0001484	X_element_combinatorial_repeat	SO:0000624
1	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	187070	SO:0001485	SO:0001485	Y_prime_element	SO:0000657
1	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	\N	telomere	SOFA	\N	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	187071	SO:0001485	SO:0001485	Y_prime_element	SO:0000624
1	"The status of whole genome sequence." [DOI:10.1126]	\N	whole_genome_sequence_status	\N	\N	sequence	"The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]	SO	187072	SO:0001486	SO:0001486	standard_draft	SO:0001499
1	"The status of whole genome sequence." [DOI:10.1126]	\N	whole_genome_sequence_status	\N	\N	sequence	"The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]	SO	187073	SO:0001487	SO:0001487	high_quality_draft	SO:0001499
1	"The status of whole genome sequence." [DOI:10.1126]	\N	whole_genome_sequence_status	\N	\N	sequence	"The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]	SO	187074	SO:0001488	SO:0001488	improved_high_quality_draft	SO:0001499
1	"The status of whole genome sequence." [DOI:10.1126]	\N	whole_genome_sequence_status	\N	\N	sequence	"The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]	SO	187075	SO:0001489	SO:0001489	annotation_directed_improved_draft	SO:0001499
1	"The status of whole genome sequence." [DOI:10.1126]	\N	whole_genome_sequence_status	\N	\N	sequence	"The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]	SO	187076	SO:0001490	SO:0001490	noncontiguous_finished	SO:0001499
1	"The status of whole genome sequence." [DOI:10.1126]	\N	whole_genome_sequence_status	\N	\N	sequence	"The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]	SO	187077	SO:0001491	SO:0001491	finished_genome	SO:0001499
1	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	\N	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	187078	SO:0001492	SO:0001492	intronic_regulatory_region	SO:0001679
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	187079	SO:0001492	SO:0001492	intronic_regulatory_region	SO:0000188
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	187080	SO:0001493	SO:0001493	centromere_DNA_Element_I	SO:0000330
1	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	\N	point_centromere	\N	\N	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	187081	SO:0001493	SO:0001493	centromere_DNA_Element_I	SO:0001794
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	187082	SO:0001494	SO:0001494	centromere_DNA_Element_II	SO:0000330
1	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	\N	point_centromere	\N	\N	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	187083	SO:0001494	SO:0001494	centromere_DNA_Element_II	SO:0001794
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	187084	SO:0001495	SO:0001495	centromere_DNA_Element_III	SO:0000330
1	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	\N	point_centromere	\N	\N	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	187085	SO:0001495	SO:0001495	centromere_DNA_Element_III	SO:0001794
1	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	187086	SO:0001496	SO:0001496	telomeric_repeat	SO:0000657
1	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	\N	telomere	SOFA	\N	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	187087	SO:0001496	SO:0001496	telomeric_repeat	SO:0000624
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	187088	SO:0001497	SO:0001497	X_element	SO:0000330
1	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	\N	telomere	SOFA	\N	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	187089	SO:0001497	SO:0001497	X_element	SO:0000624
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	187090	SO:0001498	SO:0001498	YAC_end	SO:0000150
1	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	\N	YAC	\N	\N	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	187091	SO:0001498	SO:0001498	YAC_end	SO:0000152
1	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"The status of whole genome sequence." [DOI:10.1126]	SO	187092	SO:0001499	SO:0001499	whole_genome_sequence_status	SO:0000905
1	"A measurable sequence feature that varies within a population." [SO:db]	\N	genetic_marker	\N	\N	sequence	"A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]	SO	187093	SO:0001500	SO:0001500	heritable_phenotypic_marker	SO:0001645
1	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A collection of peptide sequences." [BBOP:nlw]	SO	187094	SO:0001501	SO:0001501	peptide_collection	SO:0001260
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"An experimental feature with high sequence identity to another sequence." [SO:ke]	SO	187095	SO:0001502	SO:0001502	high_identity_region	SO:0001410
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]	SO	187096	SO:0001503	SO:0001503	processed_transcript	SO:0000673
1	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome variation derived from an event during meiosis." [SO:ke]	SO	187097	SO:0001504	SO:0001504	assortment_derived_variation	SO:0000240
1	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke]	SO	187098	SO:0001505	SO:0001505	reference_genome	SO:0001026
1	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	SO	187099	SO:0001506	SO:0001506	variant_genome	SO:0001026
1	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A collection of one or more sequences of an individual." [SO:ke]	SO	187100	SO:0001507	SO:0001507	variant_collection	SO:0001260
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	187101	SO:0001508	SO:0001508	alteration_attribute	SO:0000733
1	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	187102	SO:0001509	SO:0001509	chromosomal_variation_attribute	SO:0001508
1	"" []	\N	chromosomal_variation_attribute	\N	\N	sequence	"" []	SO	187103	SO:0001510	SO:0001510	intrachromosomal	SO:0001509
1	"" []	\N	chromosomal_variation_attribute	\N	\N	sequence	"" []	SO	187104	SO:0001511	SO:0001511	interchromosomal	SO:0001509
1	"" []	\N	alteration_attribute	\N	\N	sequence	"A quality of a chromosomal insertion,." [SO:ke]	SO	187105	SO:0001512	SO:0001512	insertion_attribute	SO:0001508
1	"A quality of a chromosomal insertion,." [SO:ke]	\N	insertion_attribute	\N	\N	sequence	"" []	SO	187106	SO:0001513	SO:0001513	tandem	SO:0001512
1	"A quality of a chromosomal insertion,." [SO:ke]	\N	insertion_attribute	\N	\N	sequence	"A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]	SO	187107	SO:0001514	SO:0001514	direct	SO:0001512
1	"A quality of a chromosomal insertion,." [SO:ke]	\N	insertion_attribute	\N	\N	sequence	"A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]	SO	187108	SO:0001515	SO:0001515	inverted	SO:0001512
1	"" []	\N	duplication_attribute	\N	\N	sequence	"The quality of a duplication where the new region exists independently of the original." [SO:ke]	SO	187109	SO:0001516	SO:0001516	free	SO:0001523
1	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	187110	SO:0001517	SO:0001517	inversion_attribute	SO:0001508
1	"" []	\N	inversion_attribute	\N	\N	sequence	"" []	SO	187111	SO:0001518	SO:0001518	pericentric	SO:0001517
1	"" []	\N	inversion_attribute	\N	\N	sequence	"" []	SO	187112	SO:0001519	SO:0001519	paracentric	SO:0001517
1	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	187113	SO:0001520	SO:0001520	translocaton_attribute	SO:0001508
1	"" []	\N	translocaton_attribute	\N	\N	sequence	"" []	SO	187114	SO:0001521	SO:0001521	reciprocal	SO:0001520
1	"" []	\N	translocaton_attribute	\N	\N	sequence	"" []	SO	187115	SO:0001522	SO:0001522	insertional	SO:0001520
1	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	187116	SO:0001523	SO:0001523	duplication_attribute	SO:0001508
1	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"" []	SO	187117	SO:0001524	SO:0001524	chromosomally_aberrant_genome	SO:0001506
1	"A region where the sequence differs from that of a specified sequence." [SO:ke]	\N	sequence_difference	SOFA	\N	sequence	"A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]	SO	187118	SO:0001525	SO:0001525	assembly_error_correction	SO:0000413
1	"A region where the sequence differs from that of a specified sequence." [SO:ke]	\N	sequence_difference	SOFA	\N	sequence	"A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]	SO	187119	SO:0001526	SO:0001526	base_call_error_correction	SO:0000413
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	SOFA	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	SO	187120	SO:0001527	SO:0001527	peptide_localization_signal	SO:0000839
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	\N	sequence	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	SO	187121	SO:0001528	SO:0001528	nuclear_localization_signal	SO:0001527
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	\N	sequence	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	SO	187122	SO:0001529	SO:0001529	endosomal_localization_signal	SO:0001527
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	\N	sequence	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	SO	187123	SO:0001530	SO:0001530	lysosomal_localization_signal	SO:0001527
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	\N	sequence	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	SO	187124	SO:0001531	SO:0001531	nuclear_export_signal	SO:0001527
1	"" []	\N	specific_recombination_site	\N	\N	sequence	"A region recognized by a recombinase." [SO:ke]	SO	187125	SO:0001532	SO:0001532	recombination_signal_sequence	SO:0000299
1	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	\N	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	187126	SO:0001533	SO:0001533	cryptic_splice_site	SO:0000162
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	\N	sequence	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	SO	187127	SO:0001534	SO:0001534	nuclear_rim_localization_signal	SO:0001527
1	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	187128	SO:0001535	SO:0001535	p_element	SO:0000182
1	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	SO	187129	SO:0001536	SO:0001536	functional_variant	SO:0001060
1	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes one or more sequence features." [SO:ke]	SO	187130	SO:0001537	SO:0001537	structural_variant	SO:0001060
1	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	SO	187131	SO:0001538	SO:0001538	transcript_function_variant	SO:0001536
1	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	SO	187132	SO:0001539	SO:0001539	translational_product_function_variant	SO:0001536
1	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant which alters the level of a transcript." [SO:ke]	SO	187133	SO:0001540	SO:0001540	level_of_transcript_variant	SO:0001538
1	"A sequence variant which alters the level of a transcript." [SO:ke]	\N	level_of_transcript_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	187134	SO:0001541	SO:0001541	decreased_transcript_level_variant	SO:0001540
1	"A sequence variant which alters the level of a transcript." [SO:ke]	\N	level_of_transcript_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	187135	SO:0001542	SO:0001542	increased_transcript_level_variant	SO:0001540
1	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	SO	187136	SO:0001543	SO:0001543	transcript_processing_variant	SO:0001538
1	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_processing_variant	\N	\N	sequence	"A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]	SO	187137	SO:0001544	SO:0001544	editing_variant	SO:0001543
1	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_processing_variant	\N	\N	sequence	"A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]	SO	187138	SO:0001545	SO:0001545	polyadenylation_variant	SO:0001543
1	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]	SO	187139	SO:0001546	SO:0001546	transcript_stability_variant	SO:0001538
1	"A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_stability_variant	\N	\N	sequence	"A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]	SO	187140	SO:0001547	SO:0001547	decreased_transcript_stability_variant	SO:0001546
1	"A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_stability_variant	\N	\N	sequence	"A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]	SO	187141	SO:0001548	SO:0001548	increased_transcript_stability_variant	SO:0001546
1	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]	SO	187142	SO:0001549	SO:0001549	transcription_variant	SO:0001538
1	"A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]	\N	transcription_variant	\N	\N	sequence	"A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]	SO	187143	SO:0001550	SO:0001550	rate_of_transcription_variant	SO:0001549
1	"A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]	\N	rate_of_transcription_variant	\N	\N	sequence	"A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	187144	SO:0001551	SO:0001551	increased_transcription_rate_variant	SO:0001550
1	"A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]	\N	rate_of_transcription_variant	\N	\N	sequence	"A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	187145	SO:0001552	SO:0001552	decreased_transcription_rate_variant	SO:0001550
1	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]	SO	187146	SO:0001553	SO:0001553	translational_product_level_variant	SO:0001539
1	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	SO	187147	SO:0001554	SO:0001554	polypeptide_function_variant	SO:0001539
1	"A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]	\N	translational_product_level_variant	\N	\N	sequence	"A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]	SO	187148	SO:0001555	SO:0001555	decreased_translational_product_level	SO:0001553
1	"A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]	\N	translational_product_level_variant	\N	\N	sequence	"A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]	SO	187149	SO:0001556	SO:0001556	increased_translational_product_level	SO:0001553
1	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	\N	polypeptide_function_variant	\N	\N	sequence	"A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]	SO	187150	SO:0001557	SO:0001557	polypeptide_gain_of_function_variant	SO:0001554
1	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	\N	polypeptide_function_variant	\N	\N	sequence	"A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]	SO	187151	SO:0001558	SO:0001558	polypeptide_localization_variant	SO:0001554
1	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	\N	polypeptide_function_variant	\N	\N	sequence	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	SO	187152	SO:0001559	SO:0001559	polypeptide_loss_of_function_variant	SO:0001554
1	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	\N	polypeptide_loss_of_function_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]	SO	187153	SO:0001560	SO:0001560	inactive_ligand_binding_site	SO:0001559
1	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	\N	polypeptide_loss_of_function_variant	\N	\N	sequence	"A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]	SO	187154	SO:0001561	SO:0001561	polypeptide_partial_loss_of_function	SO:0001559
1	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	\N	polypeptide_function_variant	\N	\N	sequence	"A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]	SO	187155	SO:0001562	SO:0001562	polypeptide_post_translational_processing_variant	SO:0001554
1	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]	SO	187156	SO:0001563	SO:0001563	copy_number_change	SO:0001537
1	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant where the structure of the gene is changed." [SO:ke]	SO	187157	SO:0001564	SO:0001564	gene_variant	SO:0001878
1	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby a two genes have become joined." [SO:ke]	SO	187158	SO:0001565	SO:0001565	gene_fusion	SO:0001564
1	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located within a regulatory region." [SO:ke]	SO	187159	SO:0001566	SO:0001566	regulatory_region_variant	SO:0001878
1	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	\N	terminator_codon_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	187160	SO:0001567	SO:0001567	stop_retained_variant	SO:0001590
1	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	\N	synonymous_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	187161	SO:0001567	SO:0001567	stop_retained_variant	SO:0001819
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes the process of splicing." [SO:ke]	SO	187162	SO:0001568	SO:0001568	splicing_variant	SO:0001576
1	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	187163	SO:0001569	SO:0001569	cryptic_splice_site_variant	SO:0001568
1	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	cryptic_splice_site_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	SO	187164	SO:0001570	SO:0001570	cryptic_splice_acceptor	SO:0001569
1	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	cryptic_splice_site_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	SO	187165	SO:0001571	SO:0001571	cryptic_splice_donor	SO:0001569
1	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant whereby an exon is lost from the transcript." [SO:ke]	SO	187166	SO:0001572	SO:0001572	exon_loss_variant	SO:0001568
1	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	187167	SO:0001573	SO:0001573	intron_gain	SO:0001568
1	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	\N	splice_site_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	187168	SO:0001574	SO:0001574	splice_acceptor_variant	SO:0001629
1	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	\N	splice_site_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	187169	SO:0001575	SO:0001575	splice_donor_variant	SO:0001629
1	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that changes the structure of the transcript." [SO:ke]	SO	187170	SO:0001576	SO:0001576	transcript_variant	SO:0001564
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]	SO	187171	SO:0001577	SO:0001577	complex_transcript_variant	SO:0001576
1	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	\N	terminator_codon_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	187172	SO:0001578	SO:0001578	stop_lost	SO:0001590
1	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_elongation	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	187173	SO:0001578	SO:0001578	stop_lost	SO:0001907
1	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	187174	SO:0001578	SO:0001578	stop_lost	SO:0001992
1	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	187175	SO:0001580	SO:0001580	coding_sequence_variant	SO:0001791
1	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	187176	SO:0001580	SO:0001580	coding_sequence_variant	SO:0001968
1	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	187177	SO:0001582	SO:0001582	initiator_codon_variant	SO:0001580
1	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	187178	SO:0001583	SO:0001583	missense_variant	SO:0001992
1	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	\N	missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	187179	SO:0001585	SO:0001585	conservative_missense_variant	SO:0001583
1	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	\N	missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	187180	SO:0001586	SO:0001586	non_conservative_missense_variant	SO:0001583
1	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_truncation	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	187181	SO:0001587	SO:0001587	stop_gained	SO:0001906
1	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	187182	SO:0001587	SO:0001587	stop_gained	SO:0001992
1	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	187183	SO:0001589	SO:0001589	frameshift_variant	SO:0001818
1	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	187184	SO:0001590	SO:0001590	terminator_codon_variant	SO:0001580
1	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	\N	frameshift_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	187185	SO:0001591	SO:0001591	frame_restoring_variant	SO:0001589
1	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	\N	frameshift_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	187186	SO:0001592	SO:0001592	minus_1_frameshift_variant	SO:0001589
1	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	\N	frameshift_variant	\N	\N	sequence	"" []	SO	187187	SO:0001593	SO:0001593	minus_2_frameshift_variant	SO:0001589
1	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	\N	frameshift_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	187188	SO:0001594	SO:0001594	plus_1_frameshift_variant	SO:0001589
1	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	\N	frameshift_variant	\N	\N	sequence	"" []	SO	187189	SO:0001595	SO:0001595	plus_2_frameshift_variant	SO:0001589
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]	SO	187190	SO:0001596	SO:0001596	transcript_secondary_structure_variant	SO:0001576
1	"A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]	\N	transcript_secondary_structure_variant	\N	\N	sequence	"A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]	SO	187191	SO:0001597	SO:0001597	compensatory_transcript_secondary_structure_variant	SO:0001596
1	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	SO	187192	SO:0001598	SO:0001598	translational_product_structure_variant	SO:0001564
1	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	187193	SO:0001599	SO:0001599	3D_polypeptide_structure_variant	SO:0001539
1	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	\N	3D_polypeptide_structure_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	187194	SO:0001600	SO:0001600	complex_3D_structural_variant	SO:0001599
1	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	\N	3D_polypeptide_structure_variant	\N	\N	sequence	"A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]	SO	187195	SO:0001601	SO:0001601	conformational_change_variant	SO:0001599
1	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"" []	SO	187196	SO:0001602	SO:0001602	complex_change_of_translational_product_variant	SO:0001539
1	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	SO	187197	SO:0001603	SO:0001603	polypeptide_sequence_variant	SO:0001598
1	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]	SO	187198	SO:0001604	SO:0001604	amino_acid_deletion	SO:0001603
1	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]	SO	187199	SO:0001605	SO:0001605	amino_acid_insertion	SO:0001603
1	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	SO	187200	SO:0001606	SO:0001606	amino_acid_substitution	SO:0001603
1	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	\N	amino_acid_substitution	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	SO	187201	SO:0001607	SO:0001607	conservative_amino_acid_substitution	SO:0001606
1	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	\N	amino_acid_substitution	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	SO	187202	SO:0001608	SO:0001608	non_conservative_amino_acid_substitution	SO:0001606
1	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	SO	187203	SO:0001609	SO:0001609	elongated_polypeptide	SO:0001603
1	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	\N	elongated_polypeptide	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	187204	SO:0001610	SO:0001610	elongated_polypeptide_C_terminal	SO:0001609
1	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	\N	elongated_polypeptide	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	187205	SO:0001611	SO:0001611	elongated_polypeptide_N_terminal	SO:0001609
1	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	\N	elongated_polypeptide_C_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	187206	SO:0001612	SO:0001612	elongated_in_frame_polypeptide_C_terminal	SO:0001610
1	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	\N	elongated_polypeptide_C_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	187207	SO:0001613	SO:0001613	elongated_out_of_frame_polypeptide_C_terminal	SO:0001610
1	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	\N	elongated_polypeptide_N_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	187208	SO:0001614	SO:0001614	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001611
1	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	\N	elongated_polypeptide_N_terminal	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	187209	SO:0001615	SO:0001615	elongated_out_of_frame_polypeptide_N_terminal	SO:0001611
1	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]	SO	187210	SO:0001616	SO:0001616	polypeptide_fusion	SO:0001603
1	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]	SO	187211	SO:0001617	SO:0001617	polypeptide_truncation	SO:0001603
1	"A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]	\N	inactive_ligand_binding_site	\N	\N	sequence	"A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]	SO	187212	SO:0001618	SO:0001618	inactive_catalytic_site	SO:0001560
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant of a non coding RNA gene." [SO:ke]	SO	187213	SO:0001619	SO:0001619	non_coding_transcript_variant	SO:0001576
1	"A transcript variant of a non coding RNA gene." [SO:ke]	\N	non_coding_transcript_variant	\N	\N	sequence	"A transcript variant located with the sequence of the mature miRNA." [SO:ke]	SO	187214	SO:0001620	SO:0001620	mature_miRNA_variant	SO:0001619
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A variant in a transcript that is the target of NMD." [SO:ke]	SO	187215	SO:0001621	SO:0001621	NMD_transcript_variant	SO:0001576
1	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	187216	SO:0001622	SO:0001622	UTR_variant	SO:0001791
1	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	187217	SO:0001622	SO:0001622	UTR_variant	SO:0001968
1	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	187218	SO:0001623	SO:0001623	5_prime_UTR_variant	SO:0001622
1	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	187219	SO:0001624	SO:0001624	3_prime_UTR_variant	SO:0001622
1	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	\N	terminator_codon_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	187220	SO:0001626	SO:0001626	incomplete_terminal_codon_variant	SO:0001590
1	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	187221	SO:0001626	SO:0001626	incomplete_terminal_codon_variant	SO:0001650
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant occurring within an intron." [SO:ke]	SO	187222	SO:0001627	SO:0001627	intron_variant	SO:0001576
1	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located in the intergenic region, between genes." [SO:ke]	SO	187223	SO:0001628	SO:0001628	intergenic_variant	SO:0001878
1	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	187224	SO:0001629	SO:0001629	splice_site_variant	SO:0001568
1	"A transcript variant occurring within an intron." [SO:ke]	\N	intron_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	187225	SO:0001629	SO:0001629	splice_site_variant	SO:0001627
1	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]	SO	187226	SO:0001630	SO:0001630	splice_region_variant	SO:0001568
1	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A sequence variant located 5' of a gene." [SO:ke]	SO	187227	SO:0001631	SO:0001631	upstream_gene_variant	SO:0001628
1	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A sequence variant located 3' of a gene." [SO:ke]	SO	187228	SO:0001632	SO:0001632	downstream_gene_variant	SO:0001628
1	"A sequence variant located 3' of a gene." [SO:ke]	\N	downstream_gene_variant	\N	\N	sequence	"A sequence variant located within 5 KB of the end of a gene." [SO:ke]	SO	187229	SO:0001633	SO:0001633	5KB_downstream_variant	SO:0001632
1	"A sequence variant located within 5 KB of the end of a gene." [SO:ke]	\N	5KB_downstream_variant	\N	\N	sequence	"A sequence variant located within a half KB of the end of a gene." [SO:ke]	SO	187230	SO:0001634	SO:0001634	500B_downstream_variant	SO:0001633
1	"A sequence variant located 5' of a gene." [SO:ke]	\N	upstream_gene_variant	\N	\N	sequence	"A sequence variant located within 5KB 5' of a gene." [SO:ke]	SO	187231	SO:0001635	SO:0001635	5KB_upstream_variant	SO:0001631
1	"A sequence variant located within 5KB 5' of a gene." [SO:ke]	\N	5KB_upstream_variant	\N	\N	sequence	"A sequence variant located within 2KB 5' of a gene." [SO:ke]	SO	187232	SO:0001636	SO:0001636	2KB_upstream_variant	SO:0001635
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"A gene that encodes for ribosomal RNA." [SO:ke]	SO	187233	SO:0001637	SO:0001637	rRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"A gene that encodes for an piwi associated RNA." [SO:ke]	SO	187234	SO:0001638	SO:0001638	piRNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"A gene that encodes an RNase P RNA." [SO:ke]	SO	187235	SO:0001639	SO:0001639	RNase_P_RNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"A gene that encodes a RNase_MRP_RNA." [SO:ke]	SO	187236	SO:0001640	SO:0001640	RNase_MRP_RNA_gene	SO:0001263
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"A gene that encodes large intervening non-coding RNA." [SO:ke]	SO	187237	SO:0001641	SO:0001641	lincRNA_gene	SO:0001263
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill]	SO	187238	SO:0001642	SO:0001642	mathematically_defined_repeat	SO:0001410
1	"" []	\N	ncRNA_gene	\N	\N	sequence	"A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]	SO	187239	SO:0001643	SO:0001643	telomerase_RNA_gene	SO:0001263
1	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	187240	SO:0001644	SO:0001644	targeting_vector	SO:0000440
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	187241	SO:0001644	SO:0001644	targeting_vector	SO:0000804
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A measurable sequence feature that varies within a population." [SO:db]	SO	187242	SO:0001645	SO:0001645	genetic_marker	SO:0001411
1	"A measurable sequence feature that varies within a population." [SO:db]	\N	genetic_marker	\N	\N	sequence	"A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]	SO	187243	SO:0001646	SO:0001646	DArT_marker	SO:0001645
1	"Region in mRNA where ribosome assembles." [SO:ke]	SOFA	ribosome_entry_site	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	187244	SO:0001647	SO:0001647	kozak_sequence	SO:0000139
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposon that is disrupted by the insertion of another element." [SO:ke]	SO	187245	SO:0001648	SO:0001648	nested_transposon	SO:0000101
1	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A repeat that is disrupted by the insertion of another element." [SO:ke]	SO	187246	SO:0001649	SO:0001649	nested_repeat	SO:0000657
1	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	187247	SO:0001650	SO:0001650	inframe_variant	SO:0001818
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	187248	SO:0001653	SO:0001653	retinoic_acid_responsive_element	SO:0000713
1	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	187249	SO:0001653	SO:0001653	retinoic_acid_responsive_element	SO:0000167
1	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SOFA	protein_binding_site	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	187250	SO:0001654	SO:0001654	nucleotide_to_protein_binding_site	SO:0000410
1	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	SO	187251	SO:0001655	SO:0001655	nucleotide_binding_site	SO:0000409
1	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	SO	187252	SO:0001656	SO:0001656	metal_binding_site	SO:0000409
1	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]	SO	187253	SO:0001657	SO:0001657	ligand_binding_site	SO:0000409
1	"A repeat that is disrupted by the insertion of another element." [SO:ke]	\N	nested_repeat	\N	\N	sequence	"An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]	SO	187254	SO:0001658	SO:0001658	nested_tandem_repeat	SO:0001649
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"" []	SO	187255	SO:0001659	SO:0001659	promoter_element	SO:0000713
1	"" []	\N	promoter_element	\N	\N	sequence	"" []	SO	187256	SO:0001660	SO:0001660	core_promoter_element	SO:0001659
1	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	\N	TATA_box	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	187257	SO:0001661	SO:0001661	RNA_polymerase_II_TATA_box	SO:0000174
1	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	187258	SO:0001661	SO:0001661	RNA_polymerase_II_TATA_box	SO:0001669
1	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	\N	TATA_box	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	187259	SO:0001662	SO:0001662	RNA_polymerase_III_TATA_box	SO:0000174
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	187260	SO:0001662	SO:0001662	RNA_polymerase_III_TATA_box	SO:0000171
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	187261	SO:0001663	SO:0001663	BREd_motif	SO:0001660
1	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	187262	SO:0001663	SO:0001663	BREd_motif	SO:0001669
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	187263	SO:0001664	SO:0001664	DCE	SO:0001660
1	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	187264	SO:0001664	SO:0001664	DCE	SO:0001669
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	187265	SO:0001665	SO:0001665	DCE_SI	SO:0000713
1	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	\N	DCE	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	187266	SO:0001665	SO:0001665	DCE_SI	SO:0001664
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	187267	SO:0001666	SO:0001666	DCE_SII	SO:0000713
1	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	\N	DCE	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	187268	SO:0001666	SO:0001666	DCE_SII	SO:0001664
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	187269	SO:0001667	SO:0001667	DCE_SIII	SO:0000713
1	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	\N	DCE	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	187270	SO:0001667	SO:0001667	DCE_SIII	SO:0001664
1	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	\N	regulatory_promoter_element	\N	\N	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	187271	SO:0001668	SO:0001668	proximal_promoter_element	SO:0001678
1	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	187272	SO:0001669	SO:0001669	RNApol_II_core_promoter	SO:0000170
1	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	\N	regulatory_promoter_element	\N	\N	sequence	"" []	SO	187273	SO:0001670	SO:0001670	distal_promoter_element	SO:0001678
1	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"" []	SO	187274	SO:0001671	SO:0001671	bacterial_RNApol_promoter_sigma_70	SO:0000613
1	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"" []	SO	187275	SO:0001672	SO:0001672	bacterial_RNApol_promoter_sigma54	SO:0000613
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	187276	SO:0001673	SO:0001673	minus_12_signal	SO:0000713
1	"" []	\N	bacterial_RNApol_promoter_sigma54	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	187277	SO:0001673	SO:0001673	minus_12_signal	SO:0001672
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	187278	SO:0001674	SO:0001674	minus_24_signal	SO:0000713
1	"" []	\N	bacterial_RNApol_promoter_sigma54	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	187279	SO:0001674	SO:0001674	minus_24_signal	SO:0001672
1	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	\N	A_box	\N	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	187280	SO:0001675	SO:0001675	A_box_type_1	SO:0000619
1	"" []	\N	RNApol_III_promoter_type_1	\N	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	187281	SO:0001675	SO:0001675	A_box_type_1	SO:0000617
1	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	\N	A_box	\N	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	187282	SO:0001676	SO:0001676	A_box_type_2	SO:0000619
1	"" []	\N	RNApol_III_promoter_type_2	\N	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	187283	SO:0001676	SO:0001676	A_box_type_2	SO:0000618
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	187284	SO:0001677	SO:0001677	intermediate_element	SO:0001660
1	"" []	\N	RNApol_III_promoter_type_1	\N	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	187285	SO:0001677	SO:0001677	intermediate_element	SO:0000617
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	SO	187286	SO:0001678	SO:0001678	regulatory_promoter_element	SO:0001659
1	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SO	187287	SO:0001679	SO:0001679	transcription_regulatory_region	SO:0005836
1	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	\N	sequence	"A regulatory region that is involved in the control of the process of translation." [SO:ke]	SO	187288	SO:0001680	SO:0001680	translation_regulatory_region	SO:0005836
1	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	\N	sequence	"A regulatory region that is involved in the control of the process of recombination." [SO:ke]	SO	187289	SO:0001681	SO:0001681	recombination_regulatory_region	SO:0005836
1	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	\N	sequence	"A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]	SO	187290	SO:0001682	SO:0001682	replication_regulatory_region	SO:0005836
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	SO	187291	SO:0001683	SO:0001683	sequence_motif	SO:0001411
1	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute of an experimentally derived feature." [SO:ke]	SO	187292	SO:0001684	SO:0001684	experimental_feature_attribute	SO:0000733
1	"An attribute of an experimentally derived feature." [SO:ke]	\N	experimental_feature_attribute	\N	\N	sequence	"The score of an experimentally derived feature such as a p-value." [SO:ke]	SO	187293	SO:0001685	SO:0001685	score	SO:0001684
1	"An attribute of an experimentally derived feature." [SO:ke]	\N	experimental_feature_attribute	\N	\N	sequence	"An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]	SO	187294	SO:0001686	SO:0001686	quality_value	SO:0001684
1	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	SO	187295	SO:0001687	SO:0001687	restriction_enzyme_recognition_site	SO:0001954
1	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]	SO	187296	SO:0001688	SO:0001688	restriction_enzyme_cleavage_junction	SO:0000699
1	"A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]	\N	single_strand_restriction_enzyme_cleavage_site	\N	\N	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	187297	SO:0001689	SO:0001689	five_prime_restriction_enzyme_junction	SO:0001694
1	"" []	\N	sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	187298	SO:0001689	SO:0001689	five_prime_restriction_enzyme_junction	SO:0001692
1	"A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]	\N	single_strand_restriction_enzyme_cleavage_site	\N	\N	sequence	"" []	SO	187299	SO:0001690	SO:0001690	three_prime_restriction_enzyme_junction	SO:0001694
1	"" []	\N	sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"" []	SO	187300	SO:0001690	SO:0001690	three_prime_restriction_enzyme_junction	SO:0001692
1	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"" []	SO	187301	SO:0001691	SO:0001691	blunt_end_restriction_enzyme_cleavage_site	SO:0001687
1	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"" []	SO	187302	SO:0001692	SO:0001692	sticky_end_restriction_enzyme_cleavage_site	SO:0001687
1	"The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]	\N	restriction_enzyme_cleavage_junction	\N	\N	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	187303	SO:0001693	SO:0001693	blunt_end_restriction_enzyme_cleavage_junction	SO:0001688
1	"" []	\N	blunt_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	187304	SO:0001693	SO:0001693	blunt_end_restriction_enzyme_cleavage_junction	SO:0001691
1	"The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]	\N	restriction_enzyme_cleavage_junction	\N	\N	sequence	"A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]	SO	187305	SO:0001694	SO:0001694	single_strand_restriction_enzyme_cleavage_site	SO:0001688
1	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	SO	187306	SO:0001695	SO:0001695	restriction_enzyme_single_strand_overhang	SO:0001954
1	"" []	\N	sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	SO	187307	SO:0001695	SO:0001695	restriction_enzyme_single_strand_overhang	SO:0001692
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]	SO	187308	SO:0001696	SO:0001696	experimentally_defined_binding_region	SO:0001410
1	"A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]	\N	experimentally_defined_binding_region	\N	\N	sequence	"A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]	SO	187309	SO:0001697	SO:0001697	ChIP_seq_region	SO:0001696
1	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	\N	primer	SOFA	\N	sequence	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	SO	187310	SO:0001698	SO:0001698	ASPE_primer	SO:0000112
1	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	\N	primer	SOFA	\N	sequence	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	SO	187311	SO:0001699	SO:0001699	dCAPS_primer	SO:0000112
1	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	187312	SO:0001700	SO:0001700	histone_modification	SO:0001089
1	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	187313	SO:0001700	SO:0001700	histone_modification	SO:0001720
1	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	187314	SO:0001701	SO:0001701	histone_methylation_site	SO:0001700
1	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	187315	SO:0001702	SO:0001702	histone_acetylation_site	SO:0001700
1	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	187316	SO:0001703	SO:0001703	H3K9_acetylation_site	SO:0001973
1	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	187317	SO:0001704	SO:0001704	H3K14_acetylation_site	SO:0001973
1	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	\N	H3K4_methylation_site	\N	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187318	SO:0001705	SO:0001705	H3K4_monomethylation_site	SO:0001734
1	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	\N	H3K4_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187319	SO:0001706	SO:0001706	H3K4_trimethylation	SO:0001734
1	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K9_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187320	SO:0001707	SO:0001707	H3K9_trimethylation_site	SO:0001736
1	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K27_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187321	SO:0001708	SO:0001708	H3K27_monomethylation_site	SO:0001732
1	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K27_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187322	SO:0001709	SO:0001709	H3K27_trimethylation_site	SO:0001732
1	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K79_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187323	SO:0001710	SO:0001710	H3K79_monomethylation_site	SO:0001735
1	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K79_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187324	SO:0001711	SO:0001711	H3K79_dimethylation_site	SO:0001735
1	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K79_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187325	SO:0001712	SO:0001712	H3K79_trimethylation_site	SO:0001735
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187326	SO:0001713	SO:0001713	H4K20_monomethylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	187327	SO:0001714	SO:0001714	H2BK5_monomethylation_site	SO:0001701
1	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	\N	sequence	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	SO	187328	SO:0001715	SO:0001715	ISRE	SO:0001055
1	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	187329	SO:0001716	SO:0001716	histone_ubiqitination_site	SO:0001700
1	"A histone modification site where ubiquitin may be added." [SO:ke]	\N	histone_ubiqitination_site	\N	\N	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	187330	SO:0001717	SO:0001717	H2B_ubiquitination_site	SO:0001716
1	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	187331	SO:0001718	SO:0001718	H3K18_acetylation_site	SO:0001973
1	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	187332	SO:0001719	SO:0001719	H3K23_acylation_site	SO:0001973
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SO	187333	SO:0001720	SO:0001720	epigenetically_modified_region	SO:0001411
1	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	187334	SO:0001721	SO:0001721	H3K27_acylation_site	SO:0001973
1	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K36_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	187335	SO:0001722	SO:0001722	H3K36_monomethylation_site	SO:0001733
1	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K36_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	187336	SO:0001723	SO:0001723	H3K36_dimethylation_site	SO:0001733
1	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K36_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	187337	SO:0001724	SO:0001724	H3K36_trimethylation_site	SO:0001733
1	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	\N	H3K4_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	187338	SO:0001725	SO:0001725	H3K4_dimethylation_site	SO:0001734
1	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K27_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	187339	SO:0001726	SO:0001726	H3K27_dimethylation_site	SO:0001732
1	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K9_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	187340	SO:0001727	SO:0001727	H3K9_monomethylation_site	SO:0001736
1	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	\N	H3K9_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	187341	SO:0001728	SO:0001728	H3K9_dimethylation_site	SO:0001736
1	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_4_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	187342	SO:0001729	SO:0001729	H4K16_acylation_site	SO:0001972
1	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_4_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	187343	SO:0001730	SO:0001730	H4K5_acylation_site	SO:0001972
1	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_4_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	187344	SO:0001731	SO:0001731	H4K8_acylation_site	SO:0001972
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	187345	SO:0001732	SO:0001732	H3K27_methylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	187346	SO:0001733	SO:0001733	H3K36_methylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	187347	SO:0001734	SO:0001734	H3K4_methylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	187348	SO:0001735	SO:0001735	H3K79_methylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	187349	SO:0001736	SO:0001736	H3K9_methylation_site	SO:0001701
1	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	187350	SO:0001737	SO:0001737	histone_acylation_region	SO:0001700
1	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	\N	histone_acylation_region	\N	\N	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	187351	SO:0001738	SO:0001738	H4K_acylation_region	SO:0001737
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene with a start codon other than AUG." [SO:xp]	SO	187352	SO:0001739	SO:0001739	gene_with_non_canonical_start_codon	SO:0000704
1	"A gene with a start codon other than AUG." [SO:xp]	\N	gene_with_non_canonical_start_codon	\N	\N	sequence	"A gene with a translational start codon of CUG." [SO:mc]	SO	187353	SO:0001740	SO:0001740	gene_with_start_codon_CUG	SO:0001739
1	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	\N	gene_segment	\N	\N	sequence	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	SO	187354	SO:0001741	SO:0001741	pseudogenic_gene_segment	SO:3000000
1	"A variation that increases or decreases the copy number of a given region." [SO:ke]	DBVAR	copy_number_variation	SOFA	DBVAR	sequence	"A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]	SO	187355	SO:0001742	SO:0001742	copy_number_gain	SO:0001019
1	"A variation that increases or decreases the copy number of a given region." [SO:ke]	DBVAR	copy_number_variation	SOFA	DBVAR	sequence	"A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]	SO	187356	SO:0001743	SO:0001743	copy_number_loss	SO:0001019
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR	sequence_alteration	SOFA	DBVAR	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]	SO	187357	SO:0001744	SO:0001744	UPD	SO:0001059
1	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]	\N	UPD	DBVAR	\N	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm]	SO	187358	SO:0001745	SO:0001745	maternal_uniparental_disomy	SO:0001744
1	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]	\N	UPD	DBVAR	\N	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm]	SO	187359	SO:0001746	SO:0001746	paternal_uniparental_disomy	SO:0001744
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb]	SO	187360	SO:0001747	SO:0001747	open_chromatin_region	SO:0001411
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187361	SO:0001748	SO:0001748	SL3_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187362	SO:0001749	SO:0001749	SL4_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187363	SO:0001750	SO:0001750	SL5_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187364	SO:0001751	SO:0001751	SL6_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187365	SO:0001752	SO:0001752	SL7_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187366	SO:0001753	SO:0001753	SL8_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187367	SO:0001754	SO:0001754	SL9_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187368	SO:0001755	SO:0001755	SL10_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187369	SO:0001756	SO:0001756	SL11_acceptor_site	SO:0000709
1	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	\N	SL2_acceptor_site	\N	\N	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	187370	SO:0001757	SO:0001757	SL12_acceptor_site	SO:0000709
1	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	\N	non_processed_pseudogene	\N	\N	sequence	"A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]	SO	187371	SO:0001758	SO:0001758	duplicated_pseudogene	SO:0001760
1	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	\N	non_processed_pseudogene	\N	\N	sequence	"A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]	SO	187372	SO:0001759	SO:0001759	unitary_pseudogene	SO:0001760
1	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	SO	187373	SO:0001760	SO:0001760	non_processed_pseudogene	SO:0000336
1	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	SO	187374	SO:0001761	SO:0001761	variant_quality	SO:0000400
1	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	SO	187375	SO:0001762	SO:0001762	variant_origin	SO:0001761
1	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	SO	187376	SO:0001763	SO:0001763	variant_frequency	SO:0001761
1	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	\N	variant_frequency	\N	\N	sequence	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]	SO	187377	SO:0001764	SO:0001764	unique_variant	SO:0001763
1	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	\N	variant_frequency	\N	\N	sequence	"" []	SO	187378	SO:0001765	SO:0001765	rare_variant	SO:0001763
1	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	\N	variant_frequency	\N	\N	sequence	"" []	SO	187379	SO:0001766	SO:0001766	polymorphic_variant	SO:0001763
1	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	\N	variant_frequency	\N	\N	sequence	"" []	SO	187380	SO:0001767	SO:0001767	common_variant	SO:0001763
1	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	\N	variant_frequency	\N	\N	sequence	"" []	SO	187381	SO:0001768	SO:0001768	fixed_variant	SO:0001763
1	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	SO	187382	SO:0001769	SO:0001769	variant_phenotype	SO:0001761
1	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	\N	variant_phenotype	\N	\N	sequence	"" []	SO	187383	SO:0001770	SO:0001770	benign_variant	SO:0001769
1	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	\N	variant_phenotype	\N	\N	sequence	"" []	SO	187384	SO:0001771	SO:0001771	disease_associated_variant	SO:0001769
1	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	\N	variant_phenotype	\N	\N	sequence	"" []	SO	187385	SO:0001772	SO:0001772	disease_causing_variant	SO:0001769
1	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	\N	variant_phenotype	\N	\N	sequence	"" []	SO	187386	SO:0001773	SO:0001773	lethal_variant	SO:0001769
1	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	\N	variant_phenotype	\N	\N	sequence	"" []	SO	187387	SO:0001774	SO:0001774	quantitative_variant	SO:0001769
1	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	\N	variant_origin	\N	\N	sequence	"" []	SO	187388	SO:0001775	SO:0001775	maternal_variant	SO:0001762
1	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	\N	variant_origin	\N	\N	sequence	"" []	SO	187389	SO:0001776	SO:0001776	paternal_variant	SO:0001762
1	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	\N	variant_origin	\N	\N	sequence	"" []	SO	187390	SO:0001777	SO:0001777	somatic_variant	SO:0001762
1	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	\N	variant_origin	\N	\N	sequence	"" []	SO	187391	SO:0001778	SO:0001778	germline_variant	SO:0001762
1	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	\N	variant_origin	\N	\N	sequence	"" []	SO	187392	SO:0001779	SO:0001779	pedigree_specific_variant	SO:0001762
1	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	\N	variant_origin	\N	\N	sequence	"" []	SO	187393	SO:0001780	SO:0001780	population_specific_variant	SO:0001762
1	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	\N	variant_origin	\N	\N	sequence	"" []	SO	187394	SO:0001781	SO:0001781	de_novo_variant	SO:0001762
1	"A sequence variant located within a regulatory region." [SO:ke]	\N	regulatory_region_variant	\N	\N	sequence	"A sequence variant located within a transcription factor binding site." [EBI:fc]	SO	187395	SO:0001782	SO:0001782	TF_binding_site_variant	SO:0001566
1	"" []	DBVAR	structural_alteration	DBVAR	DBVAR	sequence	"A structural sequence alteration or rearrangement encompassing one or more genome fragments." [NCBI:th, SO:ke]	SO	187396	SO:0001784	SO:0001784	complex_structural_alteration	SO:0001785
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR	sequence_alteration	SOFA	DBVAR	sequence	"" []	SO	187397	SO:0001785	SO:0001785	structural_alteration	SO:0001059
1	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	DBVAR	functional_variant	\N	DBVAR	sequence	"A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke]	SO	187398	SO:0001786	SO:0001786	loss_of_heterozygosity	SO:0001536
1	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	\N	splice_site_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	187399	SO:0001787	SO:0001787	splice_donor_5th_base_variant	SO:0001629
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	187400	SO:0001788	SO:0001788	U_box	SO:0000330
1	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	187401	SO:0001788	SO:0001788	U_box	SO:0000186
1	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	SO	187402	SO:0001789	SO:0001789	mating_type_region	SO:0005855
1	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]	SO	187403	SO:0001790	SO:0001790	paired_end_fragment	SO:0000143
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes exon sequence." [SO:ke]	SO	187404	SO:0001791	SO:0001791	exon_variant	SO:0001576
1	"A transcript variant of a non coding RNA gene." [SO:ke]	\N	non_coding_transcript_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	187405	SO:0001792	SO:0001792	non_coding_transcript_exon_variant	SO:0001619
1	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	187406	SO:0001792	SO:0001792	non_coding_transcript_exon_variant	SO:0001791
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	187407	SO:0001793	SO:0001793	clone_end	SO:0000150
1	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	187408	SO:0001793	SO:0001793	clone_end	SO:0000151
1	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	187409	SO:0001794	SO:0001794	point_centromere	SO:0000577
1	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	187410	SO:0001795	SO:0001795	regional_centromere	SO:0000577
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	187411	SO:0001796	SO:0001796	regional_centromere_central_core	SO:0000330
1	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	\N	regional_centromere	\N	\N	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	187412	SO:0001796	SO:0001796	regional_centromere_central_core	SO:0001795
1	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A repeat region found within the modular centromere." [SO:ke]	SO	187413	SO:0001797	SO:0001797	centromeric_repeat	SO:0000657
1	"A repeat region found within the modular centromere." [SO:ke]	\N	centromeric_repeat	\N	\N	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	187414	SO:0001798	SO:0001798	regional_centromere_inner_repeat_region	SO:0001797
1	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	\N	regional_centromere_central_core	\N	\N	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	187415	SO:0001798	SO:0001798	regional_centromere_inner_repeat_region	SO:0001796
1	"A repeat region found within the modular centromere." [SO:ke]	\N	centromeric_repeat	\N	\N	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	187416	SO:0001799	SO:0001799	regional_centromere_outer_repeat_region	SO:0001797
1	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	\N	regional_centromere	\N	\N	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	187417	SO:0001799	SO:0001799	regional_centromere_outer_repeat_region	SO:0001795
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	SO	187418	SO:0001800	SO:0001800	tasiRNA	SO:0000655
1	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a tasiRNA." [PMID:16145017]	SO	187419	SO:0001801	SO:0001801	tasiRNA_primary_transcript	SO:0000483
1	"A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]	\N	polyadenylation_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]	SO	187420	SO:0001802	SO:0001802	increased_polyadenylation_variant	SO:0001545
1	"A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]	\N	polyadenylation_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]	SO	187421	SO:0001803	SO:0001803	decreased_polyadenylation_variant	SO:0001545
1	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	\N	protein_protein_contact	biosapiens	\N	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	187422	SO:0001804	SO:0001804	DDB_box	SO:0001093
1	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_motif	biosapiens	\N	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	187423	SO:0001805	SO:0001805	destruction_box	SO:0100017
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	\N	sequence	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	SO	187424	SO:0001806	SO:0001806	ER_retention_signal	SO:0001527
1	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_motif	biosapiens	\N	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	187425	SO:0001807	SO:0001807	KEN_box	SO:0100017
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	\N	sequence	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	SO	187426	SO:0001808	SO:0001808	mitochondrial_targeting_signal	SO:0001527
1	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	signal_peptide	biosapiens,SOFA	\N	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	187427	SO:0001809	SO:0001809	signal_anchor	SO:0000418
1	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	\N	protein_protein_contact	biosapiens	\N	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	187428	SO:0001810	SO:0001810	PIP_box	SO:0001093
1	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	187429	SO:0001811	SO:0001811	phosphorylation_site	SO:0001089
1	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	\N	peptide_helix	biosapiens	\N	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	187430	SO:0001812	SO:0001812	transmembrane_helix	SO:0001114
1	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	\N	transmembrane_polypeptide_region	biosapiens	\N	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	187431	SO:0001812	SO:0001812	transmembrane_helix	SO:0001077
1	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	\N	sequence	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	SO	187432	SO:0001813	SO:0001813	vacuolar_sorting_signal	SO:0001527
1	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	187433	SO:0001814	SO:0001814	coding_variant_quality	SO:0001761
1	"" []	\N	coding_variant_quality	\N	\N	sequence	"" []	SO	187434	SO:0001815	SO:0001815	synonymous	SO:0001814
1	"" []	\N	coding_variant_quality	\N	\N	sequence	"" []	SO	187435	SO:0001816	SO:0001816	non_synonymous	SO:0001814
1	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]	SO	187436	SO:0001817	SO:0001817	inframe	SO:0000863
1	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	187437	SO:0001818	SO:0001818	protein_altering_variant	SO:0001580
1	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	187438	SO:0001819	SO:0001819	synonymous_variant	SO:0001580
1	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	187439	SO:0001820	SO:0001820	inframe_indel	SO:0001650
1	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	\N	inframe_indel	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	187440	SO:0001821	SO:0001821	inframe_insertion	SO:0001820
1	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	\N	internal_feature_elongation	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	187441	SO:0001821	SO:0001821	inframe_insertion	SO:0001908
1	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	\N	inframe_indel	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	187442	SO:0001822	SO:0001822	inframe_deletion	SO:0001820
1	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_truncation	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	187443	SO:0001822	SO:0001822	inframe_deletion	SO:0001906
1	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	\N	inframe_insertion	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	187444	SO:0001823	SO:0001823	conservative_inframe_insertion	SO:0001821
1	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	\N	inframe_insertion	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	187445	SO:0001824	SO:0001824	disruptive_inframe_insertion	SO:0001821
1	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	\N	inframe_deletion	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	187446	SO:0001825	SO:0001825	conservative_inframe_deletion	SO:0001822
1	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	\N	inframe_deletion	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	187447	SO:0001826	SO:0001826	disruptive_inframe_deletion	SO:0001822
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	187448	SO:0001827	SO:0001827	mRNA_read	SO:0000150
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	187449	SO:0001828	SO:0001828	genomic_DNA_read	SO:0000150
1	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	\N	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	187450	SO:0001829	SO:0001829	mRNA_contig	SO:0000149
1	"A region amplified by a PCR reaction." [SO:ke]	\N	PCR_product	SOFA	\N	sequence	"A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]	SO	187451	SO:0001830	SO:0001830	AFLP_fragment	SO:0000006
1	"A match against a protein sequence." [SO:ke]	\N	protein_match	SOFA	\N	sequence	"A match to a protein HMM such as pfam." [SO:ke]	SO	187452	SO:0001831	SO:0001831	protein_hmm_match	SO:0000349
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	\N	sequence	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	SO	187453	SO:0001832	SO:0001832	immunoglobulin_region	SO:0000839
1	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	\N	immunoglobulin_region	\N	\N	sequence	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	187454	SO:0001833	SO:0001833	V_region	SO:0001832
1	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	\N	immunoglobulin_region	\N	\N	sequence	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	187455	SO:0001834	SO:0001834	C_region	SO:0001832
1	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	187456	SO:0001835	SO:0001835	N_region	SO:0000301
1	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	187457	SO:0001836	SO:0001836	S_region	SO:0000301
1	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	\N	insertion	DBVAR,SOFA	\N	sequence	"A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]	SO	187458	SO:0001837	SO:0001837	mobile_element_insertion	SO:0000667
1	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	\N	insertion	DBVAR,SOFA	\N	sequence	"An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]	SO	187459	SO:0001838	SO:0001838	novel_sequence_insertion	SO:0000667
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	SO	187460	SO:0001839	SO:0001839	CSL_response_element	SO:0001659
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	187461	SO:0001840	SO:0001840	GATA_box	SO:0001660
1	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]	SO	187462	SO:0001841	SO:0001841	polymorphic_pseudogene	SO:0000336
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	SO	187463	SO:0001842	SO:0001842	AP_1_binding_site	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	SO	187464	SO:0001843	SO:0001843	CRE	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	SO	187465	SO:0001844	SO:0001844	CuRE	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	SO	187466	SO:0001845	SO:0001845	DRE	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	SO	187467	SO:0001846	SO:0001846	FLEX_element	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	SO	187468	SO:0001847	SO:0001847	forkhead_motif	SO:0001659
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	187469	SO:0001848	SO:0001848	homol_D_box	SO:0001660
1	"" []	\N	promoter_element	\N	\N	sequence	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	SO	187470	SO:0001849	SO:0001849	homol_E_box	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	SO	187471	SO:0001850	SO:0001850	HSE	SO:0001659
1	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	\N	GATA_box	\N	\N	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	187472	SO:0001851	SO:0001851	iron_repressed_GATA_element	SO:0001840
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	SO	187473	SO:0001852	SO:0001852	mating_type_M_box	SO:0001659
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]	SO	187474	SO:0001853	SO:0001853	androgen_response_element	SO:0000713
1	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	\N	probe	\N	\N	sequence	"A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]	SO	187475	SO:0001854	SO:0001854	smFISH_probe	SO:0000051
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	SO	187476	SO:0001855	SO:0001855	MCB	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	SO	187477	SO:0001856	SO:0001856	CCAAT_motif	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	SO	187478	SO:0001857	SO:0001857	Ace2_UAS	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	SO	187479	SO:0001858	SO:0001858	TR_box	SO:0001659
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	SO	187480	SO:0001859	SO:0001859	STREP_motif	SO:0001659
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]	SO	187481	SO:0001860	SO:0001860	rDNA_intergenic_spacer_element	SO:0000713
1	"" []	\N	promoter_element	\N	\N	sequence	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	SO	187482	SO:0001861	SO:0001861	sterol_regulatory_element	SO:0001659
1	"" []	\N	dinucleotide_repeat_microsatellite_feature	\N	\N	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	187483	SO:0001862	SO:0001862	GT_dinucleotide_repeat	SO:0000290
1	"" []	\N	trinucleotide_repeat_microsatellite_feature	\N	\N	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	187484	SO:0001863	SO:0001863	GTT_trinucleotide_repeat	SO:0000291
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]	SO	187485	SO:0001864	SO:0001864	Sap1_recognition_motif	SO:0000713
1	"" []	\N	promoter_element	\N	\N	sequence	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	SO	187486	SO:0001865	SO:0001865	CDRE_motif	SO:0001659
1	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	\N	sequence	"A contig of BAC reads." [GMOD:ea]	SO	187487	SO:0001866	SO:0001866	BAC_read_contig	SO:0000149
1	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	\N	BAC	\N	\N	sequence	"A contig of BAC reads." [GMOD:ea]	SO	187488	SO:0001866	SO:0001866	BAC_read_contig	SO:0000153
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene suspected of being involved in the expression of a trait." [GMOD:ea]	SO	187489	SO:0001867	SO:0001867	candidate_gene	SO:0000704
1	"A gene suspected of being involved in the expression of a trait." [GMOD:ea]	\N	candidate_gene	\N	\N	sequence	"A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]	SO	187490	SO:0001868	SO:0001868	positional_candidate_gene	SO:0001867
1	"A gene suspected of being involved in the expression of a trait." [GMOD:ea]	\N	candidate_gene	\N	\N	sequence	"A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]	SO	187491	SO:0001869	SO:0001869	functional_candidate_gene	SO:0001867
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	SO	187492	SO:0001870	SO:0001870	enhancerRNA	SO:0000655
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	SO	187493	SO:0001871	SO:0001871	PCB	SO:0001659
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	SO	187494	SO:0001872	SO:0001872	rearrangement_breakpoint	SO:0001411
1	"" []	\N	structural_alteration	DBVAR	\N	sequence	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	SO	187495	SO:0001872	SO:0001872	rearrangement_breakpoint	SO:0001785
1	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	\N	rearrangement_breakpoint	\N	\N	sequence	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	SO	187496	SO:0001873	SO:0001873	interchromosomal_breakpoint	SO:0001872
1	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	\N	rearrangement_breakpoint	\N	\N	sequence	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	SO	187497	SO:0001874	SO:0001874	intrachromosomal_breakpoint	SO:0001872
1	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	\N	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	187498	SO:0001875	SO:0001875	unassigned_supercontig	SO:0000148
1	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SO	187499	SO:0001876	SO:0001876	partial_genomic_sequence_assembly	SO:0000353
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	SO	187500	SO:0001877	SO:0001877	lnc_RNA	SO:0000655
1	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	SO	187501	SO:0001878	SO:0001878	feature_variant	SO:0001537
1	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]	SO	187502	SO:0001879	SO:0001879	feature_ablation	SO:0001537
1	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]	SO	187503	SO:0001880	SO:0001880	feature_amplification	SO:0001537
1	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]	SO	187504	SO:0001881	SO:0001881	feature_translocation	SO:0001537
1	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]	SO	187505	SO:0001882	SO:0001882	feature_fusion	SO:0001537
1	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_translocation	\N	\N	sequence	"A feature translocation where the region contains a transcript." [SO:ke]	SO	187506	SO:0001883	SO:0001883	transcript_translocation	SO:0001881
1	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_translocation	\N	\N	sequence	"A feature translocation where the region contains a regulatory region." [SO:ke]	SO	187507	SO:0001884	SO:0001884	regulatory_region_translocation	SO:0001881
1	"A feature translocation where the region contains a regulatory region." [SO:ke]	\N	regulatory_region_translocation	\N	\N	sequence	"A feature translocation where the region contains a transcription factor binding site." [SO:ke]	SO	187508	SO:0001885	SO:0001885	TFBS_translocation	SO:0001884
1	"A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]	\N	feature_fusion	\N	\N	sequence	"A feature fusion where the deletion brings together transcript regions." [SO:ke]	SO	187509	SO:0001886	SO:0001886	transcript_fusion	SO:0001882
1	"A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]	\N	feature_fusion	\N	\N	sequence	"A feature fusion where the deletion brings together regulatory regions." [SO:ke]	SO	187510	SO:0001887	SO:0001887	regulatory_region_fusion	SO:0001882
1	"A feature fusion where the deletion brings together regulatory regions." [SO:ke]	\N	regulatory_region_fusion	\N	\N	sequence	"A fusion where the deletion brings together transcription factor binding sites." [SO:ke]	SO	187511	SO:0001888	SO:0001888	TFBS_fusion	SO:0001887
1	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_amplification	\N	\N	sequence	"A feature amplification of a region containing a transcript." [SO:ke]	SO	187512	SO:0001889	SO:0001889	transcript_amplification	SO:0001880
1	"A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]	\N	feature_fusion	\N	\N	sequence	"A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]	SO	187513	SO:0001890	SO:0001890	transcript_regulatory_region_fusion	SO:0001882
1	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_amplification	\N	\N	sequence	"A feature amplification of a region containing a regulatory region." [SO:ke]	SO	187514	SO:0001891	SO:0001891	regulatory_region_amplification	SO:0001880
1	"A feature amplification of a region containing a regulatory region." [SO:ke]	\N	regulatory_region_amplification	\N	\N	sequence	"A feature amplification of a region containing a transcription factor binding site." [SO:ke]	SO	187515	SO:0001892	SO:0001892	TFBS_amplification	SO:0001891
1	"A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_ablation	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]	SO	187516	SO:0001893	SO:0001893	transcript_ablation	SO:0001879
1	"A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_ablation	\N	\N	sequence	"A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]	SO	187517	SO:0001894	SO:0001894	regulatory_region_ablation	SO:0001879
1	"A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]	\N	regulatory_region_ablation	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]	SO	187518	SO:0001895	SO:0001895	TFBS_ablation	SO:0001894
1	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	187519	SO:0001896	SO:0001896	transposable_element_CDS	SO:0000316
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	187520	SO:0001896	SO:0001896	transposable_element_CDS	SO:0000101
1	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	187521	SO:0001897	SO:0001897	transposable_element_pseudogene	SO:0000336
1	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	187522	SO:0001897	SO:0001897	transposable_element_pseudogene	SO:0000101
1	"A repeat region found within the modular centromere." [SO:ke]	\N	centromeric_repeat	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	187523	SO:0001898	SO:0001898	dg_repeat	SO:0001797
1	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	\N	regional_centromere_outer_repeat_region	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	187524	SO:0001898	SO:0001898	dg_repeat	SO:0001799
1	"A repeat region found within the modular centromere." [SO:ke]	\N	centromeric_repeat	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	187525	SO:0001899	SO:0001899	dh_repeat	SO:0001797
1	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	\N	regional_centromere_outer_repeat_region	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	187526	SO:0001899	SO:0001899	dh_repeat	SO:0001799
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]	SO	187527	SO:0001900	SO:0001900	M26_binding_site	SO:0000713
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	187528	SO:0001901	SO:0001901	AACCCT_box	SO:0001660
1	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	187529	SO:0001902	SO:0001902	splice_region	SO:0000835
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	187530	SO:0001902	SO:0001902	splice_region	SO:0000185
1	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	\N	lnc_RNA	\N	\N	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	187531	SO:0001903	SO:0001903	intronic_lncRNA	SO:0001877
1	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	\N	lnc_RNA	\N	\N	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	187532	SO:0001904	SO:0001904	antisense_lncRNA	SO:0001877
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]	SO	187533	SO:0001905	SO:0001905	regional_centromere_outer_repeat_transcript	SO:0000185
1	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	SO	187534	SO:0001906	SO:0001906	feature_truncation	SO:0001878
1	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	SO	187535	SO:0001907	SO:0001907	feature_elongation	SO:0001878
1	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_elongation	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	SO	187536	SO:0001908	SO:0001908	internal_feature_elongation	SO:0001907
1	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	\N	frameshift_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	187537	SO:0001909	SO:0001909	frameshift_elongation	SO:0001589
1	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	\N	internal_feature_elongation	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	187538	SO:0001909	SO:0001909	frameshift_elongation	SO:0001908
1	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	\N	frameshift_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	187539	SO:0001910	SO:0001910	frameshift_truncation	SO:0001589
1	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_truncation	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	187540	SO:0001910	SO:0001910	frameshift_truncation	SO:0001906
1	"A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]	\N	copy_number_change	\N	\N	sequence	"A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]	SO	187541	SO:0001911	SO:0001911	copy_number_increase	SO:0001563
1	"A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]	\N	copy_number_change	\N	\N	sequence	"A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]	SO	187542	SO:0001912	SO:0001912	copy_number_decrease	SO:0001563
1	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	187543	SO:0001913	SO:0001913	bacterial_RNApol_promoter_sigma_ecf	SO:0000613
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]	SO	187544	SO:0001914	SO:0001914	rDNA_replication_fork_barrier	SO:0000713
1	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]	SO	187545	SO:0001915	SO:0001915	transcription_start_cluster	SO:0001410
1	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	\N	sequence	"A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]	SO	187546	SO:0001916	SO:0001916	CAGE_tag	SO:0000324
1	"A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]	\N	transcription_start_cluster	\N	\N	sequence	"A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]	SO	187547	SO:0001917	SO:0001917	CAGE_cluster	SO:0001915
1	"A methylated deoxy-cytosine." [SO:ke]	\N	methylated_cytosine	SOFA	\N	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	187548	SO:0001918	SO:0001918	5_methylcytosine	SO:0000114
1	"A methylated deoxy-cytosine." [SO:ke]	\N	methylated_cytosine	SOFA	\N	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	187549	SO:0001919	SO:0001919	4_methylcytosine	SO:0000114
1	"A modified  base in which adenine has been methylated." [SO:ke]	\N	methylated_adenine	SOFA	\N	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	187550	SO:0001920	SO:0001920	N6_methyladenine	SO:0000161
1	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	\N	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	187551	SO:0001921	SO:0001921	mitochondrial_contig	SO:0000149
1	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	\N	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	187552	SO:0001922	SO:0001922	mitochondrial_supercontig	SO:0000148
1	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	\N	telomeric_transcript	\N	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	187553	SO:0001923	SO:0001923	TERRA	SO:0001927
1	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	\N	telomeric_transcript	\N	\N	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	187554	SO:0001924	SO:0001924	ARRET	SO:0001927
1	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	\N	telomeric_transcript	\N	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	187555	SO:0001925	SO:0001925	ARIA	SO:0001927
1	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	\N	telomeric_transcript	\N	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	187556	SO:0001926	SO:0001926	anti_ARRET	SO:0001927
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	SO	187557	SO:0001927	SO:0001927	telomeric_transcript	SO:0000655
1	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	\N	duplication	\N	\N	sequence	"A duplication of the distal region of a chromosome." [SO:bm]	SO	187558	SO:0001928	SO:0001928	distal_duplication	SO:1000035
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	187559	SO:0001929	SO:0001929	mitochondrial_DNA_read	SO:0000150
1	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	\N	read	SOFA	\N	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	187560	SO:0001930	SO:0001930	chloroplast_DNA_read	SO:0000150
1	"" []	\N	consensus_region	\N	\N	sequence	"Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]	SO	187561	SO:0001931	SO:0001931	consensus_gDNA	SO:0000994
1	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	\N	restriction_enzyme_single_strand_overhang	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	187562	SO:0001932	SO:0001932	restriction_enzyme_five_prime_single_strand_overhang	SO:0001695
1	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	\N	restriction_enzyme_single_strand_overhang	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	187563	SO:0001933	SO:0001933	restriction_enzyme_three_prime_single_strand_overhang	SO:0001695
1	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	\N	tandem_repeat	SOFA	\N	sequence	"A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]	SO	187564	SO:0001934	SO:0001934	monomeric_repeat	SO:0000705
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	187565	SO:0001935	SO:0001935	H3K20_trimethylation_site	SO:0001701
1	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	187566	SO:0001936	SO:0001936	H3K36_acetylation_site	SO:0001973
1	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	187567	SO:0001937	SO:0001937	H2BK12_acetylation_site	SO:0001702
1	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	187568	SO:0001938	SO:0001938	H2AK5_acetylation_site	SO:0001702
1	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_4_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	187569	SO:0001939	SO:0001939	H4K12_acetylation_site	SO:0001972
1	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	187570	SO:0001940	SO:0001940	H2BK120_acetylation_site	SO:0001702
1	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_4_acylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	187571	SO:0001941	SO:0001941	H4K91_acetylation_site	SO:0001972
1	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	187572	SO:0001942	SO:0001942	H2BK20_acetylation_site	SO:0001702
1	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	187573	SO:0001943	SO:0001943	H3K4ac_acetylation_site	SO:0001973
1	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	187574	SO:0001944	SO:0001944	H2AK9_acetylation_site	SO:0001702
1	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	\N	histone_3_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	187575	SO:0001945	SO:0001945	H3K56_acetylation_site	SO:0001973
1	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	187576	SO:0001946	SO:0001946	H2BK15_acetylation_site	SO:0001702
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	187577	SO:0001947	SO:0001947	H3R2_monomethylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	187578	SO:0001948	SO:0001948	H3R2_dimethylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	187579	SO:0001949	SO:0001949	H4R3_dimethylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	187580	SO:0001950	SO:0001950	H4K4_trimethylation_site	SO:0001701
1	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	187581	SO:0001951	SO:0001951	H3K23_dimethylation_site	SO:0001701
1	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	\N	sequence	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	SO	187582	SO:0001952	SO:0001952	promoter_flanking_region	SO:0001055
1	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]	SO	187583	SO:0001953	SO:0001953	restriction_enzyme_assembly_scar	SO:0001954
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region related to restriction enzyme function." [SO:ke]	SO	187584	SO:0001954	SO:0001954	restriction_enzyme_region	SO:0001411
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	\N	sequence	"A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]	SO	187585	SO:0001955	SO:0001955	protein_stability_element	SO:0000839
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	\N	sequence	"A polypeptide_region that  codes for a protease cleavage site." [SO:ke]	SO	187586	SO:0001956	SO:0001956	protease_site	SO:0000839
1	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	187587	SO:0001958	SO:0001958	lariat_intron	SO:0000188
1	"" []	\N	core_promoter_element	\N	\N	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	187588	SO:0001959	SO:0001959	TCT_motif	SO:0001660
1	"A methylated deoxy-cytosine." [SO:ke]	\N	methylated_cytosine	SOFA	\N	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	187589	SO:0001960	SO:0001960	5_hydroxymethylcytosine	SO:0000114
1	"A modified cytosine DNA base feature." [SO:ke]	\N	modified_cytosine	\N	\N	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	187590	SO:0001961	SO:0001961	5_formylcytosine	SO:0001963
1	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A modified adenine DNA base feature." [SO:ke]	SO	187591	SO:0001962	SO:0001962	modified_adenine	SO:0000305
1	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A modified cytosine DNA base feature." [SO:ke]	SO	187592	SO:0001963	SO:0001963	modified_cytosine	SO:0000305
1	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A modified guanine DNA base feature." [SO:ke]	SO	187593	SO:0001964	SO:0001964	modified_guanine	SO:0000305
1	"A modified guanine DNA base feature." [SO:ke]	\N	modified_guanine	\N	\N	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	187594	SO:0001965	SO:0001965	8_oxoguanine	SO:0001964
1	"A modified cytosine DNA base feature." [SO:ke]	\N	modified_cytosine	\N	\N	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	187595	SO:0001966	SO:0001966	5_carboxylcytosine	SO:0001963
1	"A modified adenine DNA base feature." [SO:ke]	\N	modified_adenine	\N	\N	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	187596	SO:0001967	SO:0001967	8_oxoadenine	SO:0001962
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant of a protein coding gene." [SO:ke]	SO	187597	SO:0001968	SO:0001968	coding_transcript_variant	SO:0001576
1	"A transcript variant occurring within an intron." [SO:ke]	\N	intron_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	187598	SO:0001969	SO:0001969	coding_transcript_intron_variant	SO:0001627
1	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	187599	SO:0001969	SO:0001969	coding_transcript_intron_variant	SO:0001968
1	"A transcript variant of a non coding RNA gene." [SO:ke]	\N	non_coding_transcript_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	187600	SO:0001970	SO:0001970	non_coding_transcript_intron_variant	SO:0001619
1	"A transcript variant occurring within an intron." [SO:ke]	\N	intron_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	187601	SO:0001970	SO:0001970	non_coding_transcript_intron_variant	SO:0001627
1	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	\N	DNA_binding_site	\N	\N	sequence	"" []	SO	187602	SO:0001971	SO:0001971	zinc_finger_binding_site	SO:0001429
1	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	187603	SO:0001972	SO:0001972	histone_4_acylation_site	SO:0001702
1	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	187604	SO:0001973	SO:0001973	histone_3_acetylation_site	SO:0001702
1	"" []	\N	promoter_element	\N	\N	sequence	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	SO	187605	SO:0001974	SO:0001974	CTCF_binding_site	SO:0001659
1	"" []	\N	sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]	SO	187606	SO:0001975	SO:0001975	five_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001692
1	"" []	\N	sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]	SO	187607	SO:0001976	SO:0001976	three_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001692
1	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	\N	sequence	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	SO	187608	SO:0001977	SO:0001977	ribonuclease_site	SO:0000833
1	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A region of  sequence where developer information is encoded." [SO:ke]	SO	187609	SO:0001978	SO:0001978	signature	SO:0000804
1	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"A motif that affects the stability of RNA." [PMID:22495308, SO:ke]	SO	187610	SO:0001979	SO:0001979	RNA_stability_element	SO:0000715
1	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	\N	regulatory_promoter_element	\N	\N	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	187611	SO:0001980	SO:0001980	G_box	SO:0001678
1	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	\N	regulatory_promoter_element	\N	\N	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	187612	SO:0001981	SO:0001981	L_box	SO:0001678
1	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	\N	regulatory_promoter_element	\N	\N	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	187613	SO:0001982	SO:0001982	I-box	SO:0001678
1	"A UTR variant of the 5' UTR." [SO:ke]	\N	5_prime_UTR_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	187614	SO:0001983	SO:0001983	5_prime_UTR_premature_start_codon_variant	SO:0001623
1	"An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]	\N	gene_cassette_array	\N	\N	sequence	"A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]	SO	187615	SO:0001984	SO:0001984	silent_mating_type_cassette_array	SO:0005854
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]	SO	187616	SO:0001985	SO:0001985	Okazaki_fragment	SO:0001411
1	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]	SO	187617	SO:0001986	SO:0001986	upstream_transcript_variant	SO:0001628
1	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"" []	SO	187618	SO:0001987	SO:0001987	downstream_transcript_variant	SO:0001628
1	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	\N	5_prime_UTR_premature_start_codon_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	187619	SO:0001988	SO:0001988	5_prime_UTR_premature_start_codon_gain_variant	SO:0001983
1	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	\N	5_prime_UTR_premature_start_codon_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	187620	SO:0001989	SO:0001989	5_prime_UTR_premature_start_codon_loss_variant	SO:0001983
1	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	\N	5_prime_UTR_premature_start_codon_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	187621	SO:0001990	SO:0001990	five_prime_UTR_premature_start_codon_location_variant	SO:0001983
1	"" []	\N	consensus_region	\N	\N	sequence	"A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]	SO	187622	SO:0001991	SO:0001991	consensus_AFLP_fragment	SO:0000994
1	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	187623	SO:0001992	SO:0001992	nonsynonymous_variant	SO:0001650
1	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	\N	cis_splice_site	SOFA	\N	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	187624	SO:0001993	SO:0001993	extended_cis_splice_site	SO:0001419
1	"" []	\N	intron_domain	\N	\N	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	187625	SO:0001994	SO:0001994	intron_base_5	SO:0001014
1	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	\N	extended_cis_splice_site	\N	\N	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	187626	SO:0001994	SO:0001994	intron_base_5	SO:0001993
1	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]	SO	187627	SO:0001995	SO:0001995	extended_intronic_splice_region_variant	SO:0001568
1	"" []	\N	intron_domain	\N	\N	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	187628	SO:0001996	SO:0001996	extended_intronic_splice_region	SO:0001014
1	"" []	\N	chromosomal_structural_element	SOFA	\N	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	187629	SO:0001997	SO:0001997	subtelomere	SO:0000628
1	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]	SO	187630	SO:0001998	SO:0001998	sgRNA	SO:0000696
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	187631	SO:0001999	SO:0001999	mating_type_region_motif	SO:0000713
1	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	\N	mating_type_region	\N	\N	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	187632	SO:0001999	SO:0001999	mating_type_region_motif	SO:0001789
1	"DNA motif that is a component of a mating type region." [SO:ke]	\N	mating_type_region_motif	\N	\N	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	187633	SO:0002000	SO:0002000	W_region	SO:0001999
1	"DNA motif that is a component of a mating type region." [SO:ke]	\N	mating_type_region_motif	\N	\N	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	187634	SO:0002001	SO:0002001	Y_region	SO:0001999
1	"DNA motif that is a component of a mating type region." [SO:ke]	\N	mating_type_region_motif	\N	\N	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	187635	SO:0002002	SO:0002002	Z1_region	SO:0001999
1	"DNA motif that is a component of a mating type region." [SO:ke]	\N	mating_type_region_motif	\N	\N	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	187636	SO:0002003	SO:0002003	Z2_region	SO:0001999
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	187637	SO:0002004	SO:0002004	ARS_consensus_sequence	SO:0000713
1	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	\N	ARS	SOFA	\N	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	187638	SO:0002004	SO:0002004	ARS_consensus_sequence	SO:0000436
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]	SO	187639	SO:0002005	SO:0002005	DSR_motif	SO:0000713
1	"" []	\N	promoter_element	\N	\N	sequence	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	SO	187640	SO:0002006	SO:0002006	zinc_repressed_element	SO:0001659
1	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	\N	sequence	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	SO	187641	SO:0002007	SO:0002007	MNV	SO:1000002
1	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	\N	non_conservative_missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	187642	SO:0002008	SO:0002008	rare_amino_acid_variant	SO:0001586
1	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	\N	rare_amino_acid_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	187643	SO:0002009	SO:0002009	selenocysteine_loss	SO:0002008
1	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	\N	rare_amino_acid_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	187644	SO:0002010	SO:0002010	pyrrolysine_loss	SO:0002008
1	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence." [SO:ke]	SO	187645	SO:0002011	SO:0002011	intragenic_variant	SO:0001576
1	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	\N	initiator_codon_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	187646	SO:0002012	SO:0002012	start_lost	SO:0001582
1	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	187647	SO:0002012	SO:0002012	start_lost	SO:0001992
1	"A UTR variant of the 5' UTR." [SO:ke]	\N	5_prime_UTR_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	187648	SO:0002013	SO:0002013	5_prime_UTR_truncation	SO:0001623
1	"A UTR variant of the 5' UTR." [SO:ke]	\N	5_prime_UTR_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	187649	SO:0002014	SO:0002014	5_prime_UTR_elongation	SO:0001623
1	"A UTR variant of the 3' UTR." [SO:ke]	\N	3_prime_UTR_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	187650	SO:0002015	SO:0002015	3_prime_UTR_truncation	SO:0001624
1	"A UTR variant of the 3' UTR." [SO:ke]	\N	3_prime_UTR_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	187651	SO:0002016	SO:0002016	3_prime_UTR_elongation	SO:0001624
1	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A sequence variant located in a conserved intergenic region, between genes." [SO:ke]	SO	187652	SO:0002017	SO:0002017	conserved_intergenic_variant	SO:0001628
1	"A transcript variant occurring within an intron." [SO:ke]	\N	intron_variant	\N	\N	sequence	"A transcript variant occurring within a conserved region of an intron." [SO:ke]	SO	187653	SO:0002018	SO:0002018	conserved_intron_variant	SO:0001627
1	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	\N	initiator_codon_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	187654	SO:0002019	SO:0002019	start_retained_variant	SO:0001582
1	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	\N	synonymous_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	187655	SO:0002019	SO:0002019	start_retained_variant	SO:0001819
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]	SO	187656	SO:0002020	SO:0002020	boundary_element	SO:0000713
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]	SO	187657	SO:0002021	SO:0002021	mating_type_region_replication_fork_barrier	SO:0000713
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	SO	187658	SO:0002022	SO:0002022	priRNA	SO:0000655
1	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	\N	sequence	"A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]	SO	187659	SO:0002023	SO:0002023	multiplexing_sequence_identifier	SO:0000324
1	"DNA motif that is a component of a mating type region." [SO:ke]	\N	mating_type_region_motif	\N	\N	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	187660	SO:0002024	SO:0002024	W_region	SO:0001999
1	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	SO	187661	SO:0002025	SO:0002025	cis_acting_homologous_chromosome_pairing_region	SO:0000713
1	"" []	\N	gene_component_region	SOFA	\N	sequence	"The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]	SO	187662	SO:0002026	SO:0002026	intein_encoding_region	SO:0000842
1	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	\N	ORF	SOFA	\N	sequence	"A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]	SO	187663	SO:0002027	SO:0002027	uORF	SO:0000236
1	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	\N	ORF	SOFA	\N	sequence	"An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]	SO	187664	SO:0002028	SO:0002028	sORF	SO:0000236
1	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	\N	ORF	SOFA	\N	sequence	"A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]	SO	187665	SO:0002029	SO:0002029	tnaORF	SO:0000236
1	"DNA motif that is a component of a mating type region." [SO:ke]	\N	mating_type_region_motif	\N	\N	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	187666	SO:0002030	SO:0002030	X_region	SO:0001999
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	SO	187667	SO:0002031	SO:0002031	shRNA	SO:0000655
1	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SO	187668	SO:0005836	SO:0005836	regulatory_region	SO:0000831
1	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	\N	snoRNA_primary_transcript	\N	\N	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	187669	SO:0005837	SO:0005837	U14_snoRNA_primary_transcript	SO:0000232
1	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	\N	C_D_box_snoRNA	SOFA	\N	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	187670	SO:0005841	SO:0005841	methylation_guide_snoRNA	SO:0000593
1	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	SO	187671	SO:0005843	SO:0005843	rRNA_cleavage_RNA	SO:0000655
1	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	\N	exon	SOFA	\N	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	187672	SO:0005845	SO:0005845	exon_of_single_exon_gene	SO:0000147
1	"" []	\N	gene_cassette_member	\N	\N	sequence	"" []	SO	187673	SO:0005847	SO:0005847	cassette_array_member	SO:0005848
1	"" []	\N	gene_array_member	\N	\N	sequence	"" []	SO	187674	SO:0005848	SO:0005848	gene_cassette_member	SO:0000081
1	"" []	\N	gene_array_member	\N	\N	sequence	"" []	SO	187675	SO:0005849	SO:0005849	gene_subarray_member	SO:0000081
1	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	\N	nucleotide_binding_site	\N	\N	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	187676	SO:0005850	SO:0005850	primer_binding_site	SO:0001655
1	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	187677	SO:0005850	SO:0005850	primer_binding_site	SO:0000186
1	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]	SO	187678	SO:0005851	SO:0005851	gene_array	SO:0005855
1	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]	SO	187679	SO:0005852	SO:0005852	gene_subarray	SO:0005855
1	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]	SO	187680	SO:0005853	SO:0005853	gene_cassette	SO:0000704
1	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]	SO	187681	SO:0005854	SO:0005854	gene_cassette_array	SO:0005855
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A collection of related genes." [SO:ma]	SO	187682	SO:0005855	SO:0005855	gene_group	SO:0001411
1	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	\N	tRNA_primary_transcript	\N	\N	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	187683	SO:0005856	SO:0005856	selenocysteine_tRNA_primary_transcript	SO:0000210
1	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	187684	SO:0005857	SO:0005857	selenocysteinyl_tRNA	SO:0000253
1	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]	SO	187685	SO:0005858	SO:0005858	syntenic_region	SO:0000330
1	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	187686	SO:0100001	SO:0100001	biochemical_region_of_peptide	SO:0001067
1	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	187687	SO:0100002	SO:0100002	molecular_contact_region	SO:0100001
1	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	SO	187688	SO:0100003	SO:0100003	intrinsically_unstructured_polypeptide_region	SO:0001070
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	187689	SO:0100004	SO:0100004	catmat_left_handed_three	SO:0001078
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	187690	SO:0100005	SO:0100005	catmat_left_handed_four	SO:0001078
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	187691	SO:0100006	SO:0100006	catmat_right_handed_three	SO:0001078
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	187692	SO:0100007	SO:0100007	catmat_right_handed_four	SO:0001078
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	187693	SO:0100008	SO:0100008	alpha_beta_motif	SO:0001078
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	187694	SO:0100009	SO:0100009	lipoprotein_signal_peptide	SO:0100011
1	"A region of sequence implicated in an experimental result." [SO:ke]	biosapiens	experimental_result_region	SOFA	biosapiens	sequence	"An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]	SO	187695	SO:0100010	SO:0100010	no_output	SO:0000703
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	187696	SO:0100011	SO:0100011	cleaved_peptide_region	SO:0000839
1	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens,SOFA	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	187697	SO:0100011	SO:0100011	cleaved_peptide_region	SO:0001063
1	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	187698	SO:0100012	SO:0100012	peptide_coil	SO:0001078
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]	SO	187699	SO:0100013	SO:0100013	hydrophobic_region_of_peptide	SO:0000839
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	187700	SO:0100014	SO:0100014	n_terminal_region	SO:0100011
1	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	biosapiens	signal_peptide	biosapiens,SOFA	biosapiens	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	187701	SO:0100014	SO:0100014	n_terminal_region	SO:0000418
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	187702	SO:0100015	SO:0100015	c_terminal_region	SO:0100011
1	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	biosapiens	signal_peptide	biosapiens,SOFA	biosapiens	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	187703	SO:0100015	SO:0100015	c_terminal_region	SO:0000418
1	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	187704	SO:0100016	SO:0100016	central_hydrophobic_region_of_signal_peptide	SO:0100011
1	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	biosapiens	signal_peptide	biosapiens,SOFA	biosapiens	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	187705	SO:0100016	SO:0100016	central_hydrophobic_region_of_signal_peptide	SO:0000418
1	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	187706	SO:0100017	SO:0100017	polypeptide_conserved_motif	SO:0001067
1	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	187707	SO:0100018	SO:0100018	polypeptide_binding_motif	SO:0100001
1	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	187708	SO:0100019	SO:0100019	polypeptide_catalytic_motif	SO:0100001
1	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	biosapiens	DNA_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	187709	SO:0100020	SO:0100020	polypeptide_DNA_contact	SO:0001429
1	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	187710	SO:0100020	SO:0100020	polypeptide_DNA_contact	SO:0100002
1	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	187711	SO:0100021	SO:0100021	polypeptide_conserved_region	SO:0000839
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SOFA	sequence_alteration	SOFA	SOFA	sequence	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SO	187712	SO:1000002	SO:1000002	substitution	SO:0001059
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SO	187713	SO:1000002	SO:1000002	substitution	SO:0001411
1	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SOFA	substitution	SOFA	SOFA	sequence	"When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	187714	SO:1000005	SO:1000005	complex_substitution	SO:1000002
1	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SOFA	SNV	SOFA	SOFA	sequence	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SO	187715	SO:1000008	SO:1000008	point_mutation	SO:0001483
1	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	187716	SO:1000009	SO:1000009	transition	SO:0001483
1	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transition	\N	\N	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	187717	SO:1000010	SO:1000010	pyrimidine_transition	SO:1000009
1	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	\N	pyrimidine_transition	\N	\N	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	187718	SO:1000011	SO:1000011	C_to_T_transition	SO:1000010
1	"A transition of a cytidine to a thymine." [SO:ke]	\N	C_to_T_transition	\N	\N	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	187719	SO:1000012	SO:1000012	C_to_T_transition_at_pCpG_site	SO:1000011
1	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	\N	pyrimidine_transition	\N	\N	sequence	"" []	SO	187720	SO:1000013	SO:1000013	T_to_C_transition	SO:1000010
1	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transition	\N	\N	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	187721	SO:1000014	SO:1000014	purine_transition	SO:1000009
1	"A substitution of a purine, A or G, for another purine." [SO:ke]	\N	purine_transition	\N	\N	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	187722	SO:1000015	SO:1000015	A_to_G_transition	SO:1000014
1	"A substitution of a purine, A or G, for another purine." [SO:ke]	\N	purine_transition	\N	\N	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	187723	SO:1000016	SO:1000016	G_to_A_transition	SO:1000014
1	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	187724	SO:1000017	SO:1000017	transversion	SO:0001483
1	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	187725	SO:1000018	SO:1000018	pyrimidine_to_purine_transversion	SO:1000017
1	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	\N	pyrimidine_to_purine_transversion	\N	\N	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	187726	SO:1000019	SO:1000019	C_to_A_transversion	SO:1000018
1	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	\N	pyrimidine_to_purine_transversion	\N	\N	sequence	"" []	SO	187727	SO:1000020	SO:1000020	C_to_G_transversion	SO:1000018
1	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	\N	pyrimidine_to_purine_transversion	\N	\N	sequence	"A transversion from T to A." [SO:ke]	SO	187728	SO:1000021	SO:1000021	T_to_A_transversion	SO:1000018
1	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	\N	pyrimidine_to_purine_transversion	\N	\N	sequence	"A transversion from T to G." [SO:ke]	SO	187729	SO:1000022	SO:1000022	T_to_G_transversion	SO:1000018
1	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	187730	SO:1000023	SO:1000023	purine_to_pyrimidine_transversion	SO:1000017
1	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	\N	purine_to_pyrimidine_transversion	\N	\N	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	187731	SO:1000024	SO:1000024	A_to_C_transversion	SO:1000023
1	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	\N	purine_to_pyrimidine_transversion	\N	\N	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	187732	SO:1000025	SO:1000025	A_to_T_transversion	SO:1000023
1	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	\N	purine_to_pyrimidine_transversion	\N	\N	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	187733	SO:1000026	SO:1000026	G_to_C_transversion	SO:1000023
1	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	\N	purine_to_pyrimidine_transversion	\N	\N	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	187734	SO:1000027	SO:1000027	G_to_T_transversion	SO:1000023
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	187735	SO:1000028	SO:1000028	intrachromosomal_mutation	SO:1000183
1	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	187736	SO:1000029	SO:1000029	chromosomal_deletion	SO:1000028
1	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	187737	SO:1000030	SO:1000030	chromosomal_inversion	SO:1000028
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	187738	SO:1000031	SO:1000031	interchromosomal_mutation	SO:1000183
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	\N	sequence	"A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel]	SO	187739	SO:1000032	SO:1000032	indel	SO:0001059
1	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	\N	insertion	DBVAR,SOFA	\N	sequence	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	SO	187740	SO:1000035	SO:1000035	duplication	SO:0000667
1	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR,SOFA	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	187741	SO:1000036	SO:1000036	inversion	SO:0001059
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	DBVAR,SOFA	biological_region	SOFA	DBVAR,SOFA	sequence	"A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	187742	SO:1000036	SO:1000036	inversion	SO:0001411
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	187743	SO:1000037	SO:1000037	chromosomal_duplication	SO:1000183
1	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	187744	SO:1000038	SO:1000038	intrachromosomal_duplication	SO:1000028
1	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	187745	SO:1000038	SO:1000038	intrachromosomal_duplication	SO:1000037
1	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	\N	tandem_duplication	DBVAR	\N	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	187746	SO:1000039	SO:1000039	direct_tandem_duplication	SO:1000173
1	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	\N	tandem_duplication	DBVAR	\N	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	187747	SO:1000040	SO:1000040	inverted_tandem_duplication	SO:1000173
1	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	187748	SO:1000041	SO:1000041	intrachromosomal_transposition	SO:0000453
1	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	187749	SO:1000041	SO:1000041	intrachromosomal_transposition	SO:1000038
1	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	187750	SO:1000041	SO:1000041	intrachromosomal_transposition	SO:1000028
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	187751	SO:1000042	SO:1000042	compound_chromosome	SO:1000183
1	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	\N	chromosomal_translocation	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	187752	SO:1000043	SO:1000043	Robertsonian_fusion	SO:1000044
1	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	187753	SO:1000044	SO:1000044	chromosomal_translocation	SO:1000031
1	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	187754	SO:1000045	SO:1000045	ring_chromosome	SO:1000028
1	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	\N	chromosomal_inversion	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	187755	SO:1000046	SO:1000046	pericentric_inversion	SO:1000030
1	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	\N	chromosomal_inversion	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	187756	SO:1000047	SO:1000047	paracentric_inversion	SO:1000030
1	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	\N	chromosomal_translocation	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	187757	SO:1000048	SO:1000048	reciprocal_chromosomal_translocation	SO:1000044
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	187758	SO:1000136	SO:1000136	autosynaptic_chromosome	SO:1000183
1	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	\N	compound_chromosome	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	187759	SO:1000138	SO:1000138	homo_compound_chromosome	SO:1000042
1	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	\N	compound_chromosome	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	187760	SO:1000140	SO:1000140	hetero_compound_chromosome	SO:1000042
1	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	187761	SO:1000141	SO:1000141	chromosome_fission	SO:1000028
1	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	\N	autosynaptic_chromosome	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	187762	SO:1000142	SO:1000142	dexstrosynaptic_chromosome	SO:1000136
1	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	\N	autosynaptic_chromosome	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	187763	SO:1000143	SO:1000143	laevosynaptic_chromosome	SO:1000136
1	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	187764	SO:1000144	SO:1000144	free_duplication	SO:1000037
1	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	\N	ring_chromosome	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	187765	SO:1000145	SO:1000145	free_ring_duplication	SO:1000045
1	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	\N	free_duplication	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	187766	SO:1000145	SO:1000145	free_ring_duplication	SO:1000144
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	187767	SO:1000146	SO:1000146	complex_chromosomal_mutation	SO:1000183
1	"An incomplete chromosome." [SO:ke]	\N	chromosomal_deletion	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	187768	SO:1000147	SO:1000147	deficient_translocation	SO:1000029
1	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	\N	chromosomal_translocation	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	187769	SO:1000147	SO:1000147	deficient_translocation	SO:1000044
1	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	\N	chromosomal_inversion	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	187770	SO:1000148	SO:1000148	inversion_cum_translocation	SO:1000030
1	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	\N	chromosomal_translocation	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	187771	SO:1000148	SO:1000148	inversion_cum_translocation	SO:1000044
1	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	187772	SO:1000148	SO:1000148	inversion_cum_translocation	SO:1000028
1	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	187773	SO:1000149	SO:1000149	bipartite_duplication	SO:1000031
1	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	187774	SO:1000149	SO:1000149	bipartite_duplication	SO:1000038
1	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	\N	chromosomal_translocation	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	187775	SO:1000150	SO:1000150	cyclic_translocation	SO:1000044
1	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	\N	chromosomal_inversion	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	187776	SO:1000151	SO:1000151	bipartite_inversion	SO:1000030
1	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	\N	insertional_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	187777	SO:1000152	SO:1000152	uninverted_insertional_duplication	SO:1000154
1	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	\N	insertional_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	187778	SO:1000153	SO:1000153	inverted_insertional_duplication	SO:1000154
1	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	187779	SO:1000154	SO:1000154	insertional_duplication	SO:1000037
1	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	187780	SO:1000155	SO:1000155	interchromosomal_transposition	SO:0000453
1	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	187781	SO:1000155	SO:1000155	interchromosomal_transposition	SO:1000031
1	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	\N	interchromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	187782	SO:1000156	SO:1000156	inverted_interchromosomal_transposition	SO:1000155
1	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	\N	interchromosomal_transposition	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	187783	SO:1000157	SO:1000157	uninverted_interchromosomal_transposition	SO:1000155
1	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	\N	intrachromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	187784	SO:1000158	SO:1000158	inverted_intrachromosomal_transposition	SO:1000041
1	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	\N	inversion_cum_translocation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	187785	SO:1000158	SO:1000158	inverted_intrachromosomal_transposition	SO:1000148
1	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	\N	intrachromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	187786	SO:1000159	SO:1000159	uninverted_intrachromosomal_transposition	SO:1000041
1	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	\N	insertional_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	187787	SO:1000160	SO:1000160	unoriented_insertional_duplication	SO:1000154
1	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	\N	interchromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	187788	SO:1000161	SO:1000161	unoriented_interchromosomal_transposition	SO:1000155
1	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	\N	intrachromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	187789	SO:1000162	SO:1000162	unoriented_intrachromosomal_transposition	SO:1000041
1	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"" []	SO	187790	SO:1000170	SO:1000170	uncharacterised_chromosomal_mutation	SO:1000183
1	"An incomplete chromosome." [SO:ke]	\N	chromosomal_deletion	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	187791	SO:1000171	SO:1000171	deficient_inversion	SO:1000029
1	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	\N	chromosomal_inversion	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	187792	SO:1000171	SO:1000171	deficient_inversion	SO:1000030
1	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	187793	SO:1000171	SO:1000171	deficient_inversion	SO:1000028
1	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	DBVAR	duplication	\N	DBVAR	sequence	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	SO	187794	SO:1000173	SO:1000173	tandem_duplication	SO:1000035
1	"" []	\N	uncharacterised_chromosomal_mutation	\N	\N	sequence	"" []	SO	187795	SO:1000175	SO:1000175	partially_characterised_chromosomal_mutation	SO:1000170
1	"" []	\N	chromosome_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	187796	SO:1000182	SO:1000182	chromosome_number_variation	SO:0000240
1	"" []	\N	chromosome_variation	\N	\N	sequence	"" []	SO	187797	SO:1000183	SO:1000183	chromosome_structure_variation	SO:0000240
1	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is alternatively spliced." [SO:xp]	SO	187798	SO:1001187	SO:1001187	alternatively_spliced_transcript	SO:0000673
1	"A gene that encodes more than one transcript." [SO:ke]	\N	encodes_alternately_spliced_transcripts	\N	\N	sequence	"A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]	SO	187799	SO:1001188	SO:1001188	encodes_1_polypeptide	SO:0000463
1	"A gene that encodes more than one transcript." [SO:ke]	\N	encodes_alternately_spliced_transcripts	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	SO	187800	SO:1001189	SO:1001189	encodes_greater_than_1_polypeptide	SO:0000463
1	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	\N	encodes_overlapping_peptides	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]	SO	187801	SO:1001190	SO:1001190	encodes_different_polypeptides_different_stop	SO:1001195
1	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	\N	encodes_overlapping_peptides	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]	SO	187802	SO:1001191	SO:1001191	encodes_overlapping_peptides_different_start	SO:1001195
1	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	\N	encodes_greater_than_1_polypeptide	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]	SO	187803	SO:1001192	SO:1001192	encodes_disjoint_polypeptides	SO:1001189
1	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	\N	encodes_overlapping_peptides	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]	SO	187804	SO:1001193	SO:1001193	encodes_overlapping_polypeptides_different_start_and_stop	SO:1001195
1	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	\N	encodes_greater_than_1_polypeptide	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	SO	187805	SO:1001195	SO:1001195	encodes_overlapping_peptides	SO:1001189
1	"A mitochondrial gene located in a maxicircle." [SO:xp]	\N	maxicircle_gene	\N	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	187806	SO:1001196	SO:1001196	cryptogene	SO:0000654
1	"A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]	\N	cryptic_gene	\N	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	187807	SO:1001196	SO:1001196	cryptogene	SO:0001431
1	"A transcript that is dicistronic." [SO:ke]	\N	dicistronic_transcript	\N	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	187808	SO:1001197	SO:1001197	dicistronic_primary_transcript	SO:0000079
1	"A primary transcript encoding for more than one gene product." [SO:ke]	\N	polycistronic_primary_transcript	\N	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	187809	SO:1001197	SO:1001197	dicistronic_primary_transcript	SO:0000631
1	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	187810	SO:1001197	SO:1001197	dicistronic_primary_transcript	SO:0000185
1	"" []	\N	gene_array_member	\N	\N	sequence	"" []	SO	187811	SO:1001217	SO:1001217	member_of_regulon	SO:0000081
1	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	187812	SO:1001246	SO:1001246	CDS_independently_known	SO:0000316
1	"A CDS that is predicted." [SO:ke]	\N	CDS_predicted	\N	\N	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	187813	SO:1001247	SO:1001247	orphan_CDS	SO:1001254
1	"A CDS that is supported by sequence similarity data." [SO:xp]	\N	CDS_supported_by_sequence_similarity_data	\N	\N	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	187814	SO:1001249	SO:1001249	CDS_supported_by_domain_match_data	SO:1001251
1	"A CDS that is predicted." [SO:ke]	\N	CDS_predicted	\N	\N	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	187815	SO:1001251	SO:1001251	CDS_supported_by_sequence_similarity_data	SO:1001254
1	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	187816	SO:1001251	SO:1001251	CDS_supported_by_sequence_similarity_data	SO:0000316
1	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is predicted." [SO:ke]	SO	187817	SO:1001254	SO:1001254	CDS_predicted	SO:0000316
1	"A CDS that is supported by sequence similarity data." [SO:xp]	\N	CDS_supported_by_sequence_similarity_data	\N	\N	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	187818	SO:1001259	SO:1001259	CDS_supported_by_EST_or_cDNA_data	SO:1001251
1	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	\N	internal_ribosome_entry_site	\N	\N	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	187819	SO:1001260	SO:1001260	internal_Shine_Dalgarno_sequence	SO:0000243
1	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	187820	SO:1001260	SO:1001260	internal_Shine_Dalgarno_sequence	SO:1001268
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	187821	SO:1001261	SO:1001261	recoded_mRNA	SO:0000234
1	"Recoding by frameshifting a particular site." [SO:ke]	\N	translationally_frameshifted	\N	\N	sequence	"An attribute describing a translational frameshift of -1." [SO:ke]	SO	187822	SO:1001262	SO:1001262	minus_1_translationally_frameshifted	SO:0000887
1	"Recoding by frameshifting a particular site." [SO:ke]	\N	translationally_frameshifted	\N	\N	sequence	"An attribute describing a translational frameshift of +1." [SO:ke]	SO	187823	SO:1001263	SO:1001263	plus_1_translationally_frameshifted	SO:0000887
1	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	\N	recoded_mRNA	\N	\N	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	187824	SO:1001264	SO:1001264	mRNA_recoded_by_translational_bypass	SO:1001261
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	187825	SO:1001264	SO:1001264	mRNA_recoded_by_translational_bypass	SO:0000234
1	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	\N	recoded_mRNA	\N	\N	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	187826	SO:1001265	SO:1001265	mRNA_recoded_by_codon_redefinition	SO:1001261
1	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	187827	SO:1001265	SO:1001265	mRNA_recoded_by_codon_redefinition	SO:0000234
1	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	187828	SO:1001268	SO:1001268	recoding_stimulatory_region	SO:0000836
1	"A start codon that is not the usual AUG sequence." [SO:ke]	\N	non_canonical_start_codon	\N	\N	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	187829	SO:1001269	SO:1001269	four_bp_start_codon	SO:0000680
1	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	\N	endonuclease_spliced_intron	\N	\N	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	187830	SO:1001271	SO:1001271	archaeal_intron	SO:0001216
1	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	\N	endonuclease_spliced_intron	\N	\N	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	187831	SO:1001272	SO:1001272	tRNA_intron	SO:0001216
1	"A start codon that is not the usual AUG sequence." [SO:ke]	\N	non_canonical_start_codon	\N	\N	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	187832	SO:1001273	SO:1001273	CTG_start_codon	SO:0000680
1	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	187833	SO:1001274	SO:1001274	SECIS_element	SO:1001268
1	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]	SO	187834	SO:1001275	SO:1001275	retron	SO:0001411
1	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	187835	SO:1001277	SO:1001277	three_prime_recoding_site	SO:1001268
1	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	\N	three_prime_recoding_site	\N	\N	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	187836	SO:1001279	SO:1001279	three_prime_stem_loop_structure	SO:1001277
1	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	187837	SO:1001280	SO:1001280	five_prime_recoding_site	SO:1001268
1	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	\N	three_prime_recoding_site	\N	\N	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	187838	SO:1001281	SO:1001281	flanking_three_prime_quadruplet_recoding_signal	SO:1001277
1	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	\N	stop_codon_signal	\N	\N	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	187839	SO:1001282	SO:1001282	UAG_stop_codon_signal	SO:1001288
1	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	\N	stop_codon_signal	\N	\N	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	187840	SO:1001283	SO:1001283	UAA_stop_codon_signal	SO:1001288
1	"A collection of related genes." [SO:ma]	SOFA	gene_group	SOFA	SOFA	sequence	"A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]	SO	187841	SO:1001284	SO:1001284	regulon	SO:0005855
1	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	\N	stop_codon_signal	\N	\N	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	187842	SO:1001285	SO:1001285	UGA_stop_codon_signal	SO:1001288
1	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	\N	three_prime_recoding_site	\N	\N	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	187843	SO:1001286	SO:1001286	three_prime_repeat_recoding_signal	SO:1001277
1	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	\N	three_prime_recoding_site	\N	\N	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	187844	SO:1001287	SO:1001287	distant_three_prime_recoding_signal	SO:1001277
1	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	187845	SO:1001288	SO:1001288	stop_codon_signal	SO:1001268
1	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]	SO	187846	SO:2000061	SO:2000061	databank_entry	SO:0000695
1	"" []	\N	gene_component_region	SOFA	\N	sequence	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	SO	187847	SO:3000000	SO:3000000	gene_segment	SO:0000842
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A folded sequence." [SO:ke]	SO	399022	SO:0000002	SO:0001411	sequence_secondary_structure	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]	SO	399023	SO:0000003	SO:0000002	G_quartet	SO:0001411
2	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"" []	SO	399024	SO:0000004	SO:0000195	interior_coding_exon	SO:0000147
2	"A region of sequence containing one or more repeat units." [SO:ke]	SOFA	repeat_region	SOFA	SOFA	sequence	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399025	SO:0000005	SO:0000705	satellite_DNA	SO:0000657
2	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A region amplified by a PCR reaction." [SO:ke]	SO	399026	SO:0000006	SO:0000695	PCR_product	SO:0001409
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	399027	SO:0000007	SO:0000150	read_pair	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SOFA	contig	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	399028	SO:0000007	SO:0000150	read_pair	SO:0000149
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	731856	SO:0000007	SO:0000149	read_pair	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SOFA	supercontig	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	731857	SO:0000007	SO:0000149	read_pair	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	731858	SO:0000007	SO:0000149	read_pair	SO:0000353
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	399032	SO:0000007	SO:0001790	read_pair	SO:0000143
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	399033	SO:0000010	SO:0000401	protein_coding	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	399034	SO:0000011	SO:0000401	non_protein_coding	SO:0000733
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	SO	399035	SO:0000012	SO:0000483	scRNA_primary_transcript	SO:0000185
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SO	399036	SO:0000013	SO:0000655	scRNA	SO:0000233
2	"" []	\N	promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	399037	SO:0000014	SO:0001660	INR_motif	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	399038	SO:0000014	SO:0001669	INR_motif	SO:0000170
2	"" []	\N	promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	399039	SO:0000015	SO:0001660	DPE_motif	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	399040	SO:0000015	SO:0001669	DPE_motif	SO:0000170
2	"" []	\N	promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	399041	SO:0000016	SO:0001660	BREu_motif	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	399042	SO:0000016	SO:0001669	BREu_motif	SO:0000170
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	399043	SO:0000017	SO:0000713	PSE_motif	SO:0000714
2	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	399044	SO:0000017	SO:0000167	PSE_motif	SO:0001055
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]	SO	399045	SO:0000018	SO:0001411	linkage_group	SO:0000001
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	SO	399046	SO:0000020	SO:0000715	RNA_internal_loop	SO:0000714
2	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	SO	399047	SO:0000021	SO:0000020	asymmetric_RNA_internal_loop	SO:0000715
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]	SO	399048	SO:0000022	SO:0000715	A_minor_RNA_motif	SO:0000714
2	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	\N	RNA_internal_loop	\N	\N	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	399049	SO:0000023	SO:0000021	K_turn_RNA_motif	SO:0000020
2	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	\N	RNA_internal_loop	\N	\N	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	399050	SO:0000024	SO:0000021	sarcin_like_RNA_motif	SO:0000020
2	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	SO	399051	SO:0000025	SO:0000020	symmetric_RNA_internal_loop	SO:0000715
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"" []	SO	399052	SO:0000026	SO:0000715	RNA_junction_loop	SO:0000714
2	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"" []	SO	399053	SO:0000027	SO:0000026	RNA_hook_turn	SO:0000715
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	399054	SO:0000028	SO:0000002	base_pair	SO:0001411
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]	SO	399055	SO:0000029	SO:0000028	WC_base_pair	SO:0000002
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A type of non-canonical base-pairing." [PMID:12177293]	SO	399056	SO:0000030	SO:0000028	sugar_edge_base_pair	SO:0000002
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	399057	SO:0000031	SO:0000696	aptamer	SO:0000695
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]	SO	399058	SO:0000032	SO:0000031	DNA_aptamer	SO:0000696
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	399059	SO:0000033	SO:0000031	RNA_aptamer	SO:0000696
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]	SO	399060	SO:0000034	SO:0001247	morpholino_oligo	SO:0000696
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	399061	SO:0000035	SO:0000836	riboswitch	SO:0000234
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	399062	SO:0000035	SO:0000836	riboswitch	SO:0000834
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	731890	SO:0000035	SO:0000234	riboswitch	SO:0000233
2	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	\N	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	399064	SO:0000036	SO:0000626	matrix_attachment_site	SO:0000830
2	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	399065	SO:0000037	SO:0000727	locus_control_region	SO:0001055
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A part of a match, for example an hsp from blast is a match_part." [SO:ke]	SO	731897	SO:0000039	SO:0001410	match_part	SO:0000001
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A part of a match, for example an hsp from blast is a match_part." [SO:ke]	SO	399067	SO:0000039	SO:0000343	match_part	SO:0001410
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A clone of a DNA region of a genome." [SO:ma]	SO	399068	SO:0000040	SO:0000151	genomic_clone	SO:0000695
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]	SO	399069	SO:0000043	SO:0000336	processed_pseudogene	SO:0001411
2	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A pseudogene caused by unequal crossing over at recombination." [SO:ke]	SO	399070	SO:0000044	SO:0001760	pseudogene_by_unequal_crossing_over	SO:0000336
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	SO	399071	SO:0000051	SO:0000696	probe	SO:0000695
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	399072	SO:0000054	SO:1000182	aneuploid	SO:0000240
2	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	chromosome_number_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	399073	SO:0000055	SO:0000054	hyperploid	SO:1000182
2	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	chromosome_number_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	399074	SO:0000056	SO:0000054	hypoploid	SO:1000182
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SO	399075	SO:0000057	SO:0000752	operator	SO:0001679
2	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SOFA	protein_binding_site	SOFA	SOFA	sequence	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SO	399076	SO:0000059	SO:0001654	nuclease_binding_site	SO:0000410
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"" []	SO	399077	SO:0000060	SO:1000042	compound_chromosome_arm	SO:1000183
2	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	nucleotide_to_protein_binding_site	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	SO	399078	SO:0000061	SO:0000059	restriction_enzyme_binding_site	SO:0001654
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	399079	SO:0000062	SO:1000029	deficient_intrachromosomal_transposition	SO:1000028
2	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	399080	SO:0000062	SO:1000041	deficient_intrachromosomal_transposition	SO:0000453
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	399081	SO:0000062	SO:1000041	deficient_intrachromosomal_transposition	SO:1000028
2	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	399082	SO:0000062	SO:1000041	deficient_intrachromosomal_transposition	SO:1000038
2	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	399083	SO:0000063	SO:1000155	deficient_interchromosomal_transposition	SO:0000453
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	399084	SO:0000063	SO:1000155	deficient_interchromosomal_transposition	SO:1000031
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	399085	SO:0000065	SO:1000183	free_chromosome_arm	SO:0000240
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	399086	SO:0000067	SO:0000401	gene_to_gene_feature	SO:0000733
2	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	SO	399087	SO:0000068	SO:0000067	overlapping	SO:0000401
2	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	SO	399088	SO:0000069	SO:0000068	inside_intron	SO:0000067
2	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]	SO	399089	SO:0000070	SO:0000069	inside_intron_antiparallel	SO:0000068
2	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	\N	overlapping	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]	SO	399090	SO:0000071	SO:0000069	inside_intron_parallel	SO:0000068
2	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]	SO	399091	SO:0000073	SO:0000068	five_prime_three_prime_overlap	SO:0000067
2	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]	SO	399092	SO:0000074	SO:0000068	five_prime_five_prime_overlap	SO:0000067
2	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]	SO	399093	SO:0000075	SO:0000068	three_prime_three_prime_overlap	SO:0000067
2	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]	SO	399094	SO:0000076	SO:0000068	three_prime_five_prime_overlap	SO:0000067
2	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]	SO	399095	SO:0000077	SO:0000068	antisense	SO:0000067
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is polycistronic." [SO:xp]	SO	399096	SO:0000078	SO:0000673	polycistronic_transcript	SO:0000831
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that is dicistronic." [SO:ke]	SO	399097	SO:0000079	SO:0000078	dicistronic_transcript	SO:0000673
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is dicistronic." [SO:ke]	SO	731929	SO:0000079	SO:0000673	dicistronic_transcript	SO:0000831
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399099	SO:0000080	SO:0000081	operon_member	SO:0000401
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	399100	SO:0000081	SO:0000401	gene_array_member	SO:0000733
2	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	399101	SO:0000083	SO:0000736	macronuclear_sequence	SO:0000735
2	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	399102	SO:0000084	SO:0000736	micronuclear_sequence	SO:0000735
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from nuclear sequence." [SO:xp]	SO	399103	SO:0000087	SO:0000704	nuclear_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene located in mitochondrial sequence." [SO:xp]	SO	399104	SO:0000088	SO:0000704	mt_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene located in kinetoplast sequence." [SO:xp]	SO	399105	SO:0000089	SO:0000088	kinetoplast_gene	SO:0000704
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from plastid sequence." [SO:xp]	SO	399106	SO:0000090	SO:0000704	plastid_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from apicoplast sequence." [SO:xp]	SO	399107	SO:0000091	SO:0000090	apicoplast_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from chloroplast sequence." [SO:xp]	SO	399108	SO:0000092	SO:0000090	ct_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from chromoplast_sequence." [SO:xp]	SO	399109	SO:0000093	SO:0000090	chromoplast_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from cyanelle sequence." [SO:xp]	SO	399110	SO:0000094	SO:0000090	cyanelle_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A plastid gene from leucoplast sequence." [SO:xp]	SO	399111	SO:0000095	SO:0000090	leucoplast_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene from proplastid sequence." [SO:ke]	SO	399112	SO:0000096	SO:0000090	proplastid_gene	SO:0000704
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from nucleomorph sequence." [SO:xp]	SO	399113	SO:0000097	SO:0000704	nucleomorph_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from plasmid sequence." [SO:xp]	SO	399114	SO:0000098	SO:0000704	plasmid_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from proviral sequence." [SO:xp]	SO	399115	SO:0000099	SO:0000704	proviral_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A proviral gene with origin endogenous retrovirus." [SO:xp]	SO	399116	SO:0000100	SO:0000099	endogenous_retroviral_gene	SO:0000704
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SOFA	mobile_genetic_element	SOFA	SOFA	sequence	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	SO	399117	SO:0000101	SO:0001039	transposable_element	SO:0001037
2	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	SOFA	sequence	"A match to an EST or cDNA sequence." [SO:ke]	SO	399118	SO:0000102	SO:0000347	expressed_sequence_match	SO:0000343
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	399119	SO:0000103	SO:0000699	clone_insert_end	SO:0000110
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SOFA	clone	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	399120	SO:0000103	SO:0000753	clone_insert_end	SO:0000151
2	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	399121	SO:0000103	SO:0000753	clone_insert_end	SO:0000695
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	SO	399122	SO:0000104	SO:0001411	polypeptide	SO:0000001
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	SO	399123	SO:0000105	SO:0000830	chromosome_arm	SO:0000340
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	SO	399124	SO:0000105	SO:0000830	chromosome_arm	SO:0001411
2	"A single stranded oligonucleotide." [SO:ke]	\N	ss_oligo	SOFA	SOFA	sequence	"" []	SO	399125	SO:0000107	SO:0000112	sequencing_primer	SO:0000441
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA with a frameshift." [SO:xp]	SO	399126	SO:0000108	SO:0000234	mRNA_with_frameshift	SO:0000233
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	399127	SO:0000111	SO:0000704	transposable_element_gene	SO:0001411
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	399128	SO:0000111	SO:0000101	transposable_element_gene	SO:0001039
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	SOFA	sequence	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	SO	399129	SO:0000112	SO:0000441	primer	SO:0000696
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SOFA	mobile_genetic_element	SOFA	SOFA	sequence	"A viral sequence which has integrated into a host genome." [SO:ke]	SO	399130	SO:0000113	SO:0001039	proviral_region	SO:0001037
2	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	modified_DNA_base	SOFA	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	399131	SO:0000114	SO:0000306	methylated_cytosine	SO:0000305
2	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	modified_DNA_base	SOFA	\N	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	399132	SO:0000114	SO:0001963	methylated_cytosine	SO:0000305
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that is modified by editing." [SO:ke]	SO	399133	SO:0000116	SO:0000237	edited	SO:0000733
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript with a translational frameshift." [SO:xp]	SO	399134	SO:0000118	SO:0000673	transcript_with_translational_frameshift	SO:0000831
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a sequence that is regulated." [SO:ke]	SO	399135	SO:0000119	SO:0000401	regulated	SO:0000733
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	SO	399136	SO:0000120	SO:0000185	protein_coding_primary_transcript	SO:0000673
2	"A single stranded oligonucleotide." [SO:ke]	\N	ss_oligo	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	399137	SO:0000121	SO:0000112	forward_primer	SO:0000441
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A folded RNA sequence." [SO:ke]	SO	399138	SO:0000122	SO:0000002	RNA_sequence_secondary_structure	SO:0001411
2	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated at transcription." [SO:ma]	SO	399139	SO:0000123	SO:0000119	transcriptionally_regulated	SO:0000401
2	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]	SO	399140	SO:0000124	SO:0000123	transcriptionally_constitutive	SO:0000119
2	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An inducer molecule is required for transcription to occur." [SO:ke]	SO	399141	SO:0000125	SO:0000123	transcriptionally_induced	SO:0000119
2	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"A repressor molecule is required for transcription to stop." [SO:ke]	SO	399142	SO:0000126	SO:0000123	transcriptionally_repressed	SO:0000119
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is silenced." [SO:xp]	SO	399143	SO:0000127	SO:0000704	silenced_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced by DNA modification." [SO:xp]	SO	399144	SO:0000128	SO:0000127	gene_silenced_by_DNA_modification	SO:0000704
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is silenced by DNA modification." [SO:xp]	SO	731977	SO:0000128	SO:0000704	gene_silenced_by_DNA_modification	SO:0001411
2	"A gene that is silenced." [SO:xp]	\N	silenced_gene	\N	\N	sequence	"A gene that is silenced by DNA methylation." [SO:xp]	SO	399146	SO:0000129	SO:0000128	gene_silenced_by_DNA_methylation	SO:0000127
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced by DNA methylation." [SO:xp]	SO	399147	SO:0000129	SO:0000128	gene_silenced_by_DNA_methylation	SO:0000704
2	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated after it has been translated." [SO:ke]	SO	399148	SO:0000130	SO:0000119	post_translationally_regulated	SO:0000401
2	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated as it is translated." [SO:ke]	SO	399149	SO:0000131	SO:0000119	translationally_regulated	SO:0000401
2	"A single stranded oligonucleotide." [SO:ke]	\N	ss_oligo	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	399150	SO:0000132	SO:0000112	reverse_primer	SO:0000441
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	SO	399151	SO:0000133	SO:0000401	epigenetically_modified	SO:0000733
2	"" []	\N	gene_attribute	\N	\N	sequence	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	SO	399152	SO:0000134	SO:0000119	genomically_imprinted	SO:0000401
2	"" []	\N	gene_attribute	\N	\N	sequence	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	SO	399153	SO:0000134	SO:0000133	genomically_imprinted	SO:0000401
2	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	399154	SO:0000135	SO:0000134	maternally_imprinted	SO:0000119
2	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	\N	epigenetically_modified	\N	\N	sequence	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	399155	SO:0000135	SO:0000134	maternally_imprinted	SO:0000133
2	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	399156	SO:0000136	SO:0000134	paternally_imprinted	SO:0000119
2	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	\N	epigenetically_modified	\N	\N	sequence	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	399157	SO:0000136	SO:0000134	paternally_imprinted	SO:0000133
2	"" []	\N	gene_attribute	\N	\N	sequence	"Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]	SO	399158	SO:0000137	SO:0000133	allelically_excluded	SO:0000401
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	SO	399159	SO:0000138	SO:0000898	gene_rearranged_at_DNA_level	SO:0000704
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	SO	399160	SO:0000138	SO:0000898	gene_rearranged_at_DNA_level	SO:0001720
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	1164903	SO:0000139	SO:0000836	ribosome_entry_site	SO:0000234
4	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	1164904	SO:0000139	SO:0000836	ribosome_entry_site	SO:0000834
2	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SOFA	UTR	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	399163	SO:0000139	SO:0000204	ribosome_entry_site	SO:0000203
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	\N	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	399164	SO:0000140	SO:0001680	attenuator	SO:0005836
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	399165	SO:0000140	SO:0000234	attenuator	SO:0000233
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399166	SO:0000141	SO:0001679	terminator	SO:0005836
2	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399167	SO:0000141	SO:0000673	terminator	SO:0000831
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A folded DNA sequence." [SO:ke]	SO	399168	SO:0000142	SO:0000002	DNA_sequence_secondary_structure	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SO	399169	SO:0000143	SO:0001410	assembly_component	SO:0000001
2	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	399170	SO:0000145	SO:0000360	recoded_codon	SO:0000851
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke]	SO	399171	SO:0000146	SO:0000237	capped	SO:0000733
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SO	399172	SO:0000147	SO:0000833	exon	SO:0000673
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SO	399173	SO:0000147	SO:0000833	exon	SO:0001411
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	\N	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	732008	SO:0000148	SO:0001876	supercontig	SO:0000353
2	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	399175	SO:0000148	SO:0000719	supercontig	SO:0001876
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	399176	SO:0000149	SO:0000143	contig	SO:0001410
5	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	1259842	SO:0000149	SO:0000353	contig	SO:0001248
2	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SOFA	ultracontig	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	399178	SO:0000149	SO:0000148	contig	SO:0000719
2	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	399179	SO:0000149	SO:0000148	contig	SO:0001876
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	732014	SO:0000150	SO:0000143	read	SO:0001410
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	399181	SO:0000150	SO:0000149	read	SO:0000143
2	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SOFA	supercontig	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	399182	SO:0000150	SO:0000149	read	SO:0000148
2	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	399183	SO:0000150	SO:0000149	read	SO:0000353
2	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SO	399184	SO:0000151	SO:0000695	clone	SO:0001409
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	399185	SO:0000152	SO:0000440	YAC	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	399186	SO:0000152	SO:0000440	YAC	SO:0001235
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	399187	SO:0000153	SO:0000440	BAC	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	399188	SO:0000153	SO:0000440	BAC	SO:0001235
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	399189	SO:0000154	SO:0000440	PAC	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	399190	SO:0000154	SO:0000440	PAC	SO:0001235
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	SO	399191	SO:0000155	SO:0001235	plasmid	SO:0001411
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	399192	SO:0000156	SO:0000440	cosmid	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	399193	SO:0000156	SO:0000440	cosmid	SO:0001235
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	399194	SO:0000157	SO:0000440	phagemid	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	399195	SO:0000157	SO:0000440	phagemid	SO:0001235
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	399196	SO:0000158	SO:0000440	fosmid	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	399197	SO:0000158	SO:0000440	fosmid	SO:0001235
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The point at which one or more contiguous nucleotides were excised." [SO:ke]	SO	399198	SO:0000159	SO:0001059	deletion	SO:0000110
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The point at which one or more contiguous nucleotides were excised." [SO:ke]	SO	399199	SO:0000159	SO:0001411	deletion	SO:0000001
2	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	modified_DNA_base	SOFA	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	399200	SO:0000161	SO:0000306	methylated_adenine	SO:0000305
2	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	modified_DNA_base	SOFA	\N	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	399201	SO:0000161	SO:0001962	methylated_adenine	SO:0000305
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	399202	SO:0000162	SO:0000835	splice_site	SO:0000185
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	399203	SO:0000162	SO:0000835	splice_site	SO:0000833
2	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SOFA	splice_site	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	399204	SO:0000163	SO:0001419	five_prime_cis_splice_site	SO:0000162
2	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SOFA	splice_site	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	399205	SO:0000164	SO:0001419	three_prime_cis_splice_site	SO:0000162
2	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SOFA	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399206	SO:0000165	SO:0000727	enhancer	SO:0001055
2	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	\N	CRM	SOFA	SOFA	sequence	"An enhancer bound by a factor." [SO:xp]	SO	399207	SO:0000166	SO:0000165	enhancer_bound_by_factor	SO:0000727
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SO	399208	SO:0000167	SO:0001055	promoter	SO:0001679
2	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	399209	SO:0000169	SO:0001203	RNApol_I_promoter	SO:0000167
2	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	399210	SO:0000170	SO:0001203	RNApol_II_promoter	SO:0000167
2	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	399211	SO:0000171	SO:0001203	RNApol_III_promoter	SO:0000167
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399212	SO:0000172	SO:0000713	CAAT_signal	SO:0000714
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399213	SO:0000172	SO:0000170	CAAT_signal	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399214	SO:0000173	SO:0001659	GC_rich_promoter_region	SO:0000713
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399215	SO:0000173	SO:0000170	GC_rich_promoter_region	SO:0001203
2	"" []	\N	promoter_element	\N	\N	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	399216	SO:0000174	SO:0001660	TATA_box	SO:0001659
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399217	SO:0000175	SO:0000713	minus_10_signal	SO:0000714
2	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399218	SO:0000175	SO:0001671	minus_10_signal	SO:0000613
2	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399219	SO:0000175	SO:0001913	minus_10_signal	SO:0000613
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399220	SO:0000176	SO:0000713	minus_35_signal	SO:0000714
2	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399221	SO:0000176	SO:0001671	minus_35_signal	SO:0000613
2	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399222	SO:0000176	SO:0001913	minus_35_signal	SO:0000613
2	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	SOFA	sequence	"A nucleotide match against a sequence from another organism." [SO:ma]	SO	399223	SO:0000177	SO:0000347	cross_genome_match	SO:0000343
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]	SO	399224	SO:0000178	SO:0005855	operon	SO:0001411
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	399225	SO:0000179	SO:0000699	clone_insert_start	SO:0000110
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SOFA	clone	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	399226	SO:0000179	SO:0000753	clone_insert_start	SO:0000151
2	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	399227	SO:0000179	SO:0000753	clone_insert_start	SO:0000695
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	SO	399228	SO:0000180	SO:0000101	retrotransposon	SO:0001039
2	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	SOFA	sequence	"A match against a translated sequence." [SO:ke]	SO	399229	SO:0000181	SO:0000347	translated_nucleotide_match	SO:0000343
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	SO	399230	SO:0000182	SO:0000101	DNA_transposon	SO:0001039
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	SOFA	gene	SOFA	SOFA	sequence	"A region of the gene which is not transcribed." [SO:ke]	SO	399231	SO:0000183	SO:0000842	non_transcribed_region	SO:0000704
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of the gene which is not transcribed." [SO:ke]	SO	399232	SO:0000183	SO:0000842	non_transcribed_region	SO:0001411
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	399233	SO:0000184	SO:0000662	U2_intron	SO:0000188
2	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SO	399234	SO:0000185	SO:0000673	primary_transcript	SO:0000831
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	399235	SO:0000186	SO:0000180	LTR_retrotransposon	SO:0000101
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399236	SO:0000188	SO:0000835	intron	SO:0000185
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399237	SO:0000188	SO:0000835	intron	SO:0000833
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	399238	SO:0000189	SO:0000180	non_LTR_retrotransposon	SO:0000101
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"" []	SO	399239	SO:0000190	SO:0000188	five_prime_intron	SO:0000835
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"" []	SO	399240	SO:0000191	SO:0000188	interior_intron	SO:0000835
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"" []	SO	399241	SO:0000192	SO:0000188	three_prime_intron	SO:0000835
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SOFA	assembly_component	SOFA	SOFA	sequence	"A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]	SO	399242	SO:0000193	SO:0000412	RFLP_fragment	SO:0000143
2	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	399243	SO:0000194	SO:0000189	LINE_element	SO:0000180
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	399244	SO:0000195	SO:0000147	coding_exon	SO:0000833
2	"A region of an exon." [RSC:cb]	SOFA	exon_region	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	399245	SO:0000196	SO:0001215	five_prime_coding_exon_coding_region	SO:0000852
2	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SOFA	coding_exon	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	399246	SO:0000196	SO:0000200	five_prime_coding_exon_coding_region	SO:0000195
2	"A region of an exon." [RSC:cb]	SOFA	exon_region	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	399247	SO:0000197	SO:0001215	three_prime_coding_exon_coding_region	SO:0000852
2	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SOFA	coding_exon	SOFA	\N	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	399248	SO:0000197	SO:0000202	three_prime_coding_exon_coding_region	SO:0000195
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"An exon that does not contain any codons." [SO:ke]	SO	399249	SO:0000198	SO:0000147	noncoding_exon	SO:0000833
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR	sequence_feature	SOFA	SOFA	sequence	"A region of nucleotide sequence that has translocated to a new position." [SO:ke]	SO	399250	SO:0000199	SO:0001059	translocation	SO:0000110
2	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	399251	SO:0000200	SO:0000195	five_prime_coding_exon	SO:0000147
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	399252	SO:0000201	SO:0000147	interior_exon	SO:0000833
2	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	\N	exon	SOFA	SOFA	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	399253	SO:0000202	SO:0000195	three_prime_coding_exon	SO:0000147
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	399254	SO:0000203	SO:0000836	UTR	SO:0000234
2	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	399255	SO:0000203	SO:0000836	UTR	SO:0000834
2	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399256	SO:0000204	SO:0000203	five_prime_UTR	SO:0000836
2	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399257	SO:0000205	SO:0000203	three_prime_UTR	SO:0000836
2	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	399258	SO:0000206	SO:0000189	SINE_element	SO:0000180
2	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	\N	sequence	"" []	SO	399259	SO:0000207	SO:0000248	simple_sequence_length_variation	SO:1000002
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	399260	SO:0000208	SO:0000182	terminal_inverted_repeat_element	SO:0000101
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SO	399261	SO:0000209	SO:0000483	rRNA_primary_transcript	SO:0000185
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	SO	399262	SO:0000210	SO:0000483	tRNA_primary_transcript	SO:0000185
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	399263	SO:0000211	SO:0000210	alanine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	399264	SO:0000212	SO:0000210	arginine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	399265	SO:0000213	SO:0000210	asparagine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	399266	SO:0000214	SO:0000210	aspartic_acid_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	399267	SO:0000215	SO:0000210	cysteine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	399268	SO:0000216	SO:0000210	glutamic_acid_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	399269	SO:0000217	SO:0000210	glutamine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	399270	SO:0000218	SO:0000210	glycine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	399271	SO:0000219	SO:0000210	histidine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	399272	SO:0000220	SO:0000210	isoleucine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	399273	SO:0000221	SO:0000210	leucine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	399274	SO:0000222	SO:0000210	lysine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	399275	SO:0000223	SO:0000210	methionine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	399276	SO:0000224	SO:0000210	phenylalanine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	399277	SO:0000225	SO:0000210	proline_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	399278	SO:0000226	SO:0000210	serine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	399279	SO:0000227	SO:0000210	threonine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	399280	SO:0000228	SO:0000210	tryptophan_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	399281	SO:0000229	SO:0000210	tyrosine_tRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	399282	SO:0000230	SO:0000210	valine_tRNA_primary_transcript	SO:0000483
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	SO	399283	SO:0000231	SO:0000483	snRNA_primary_transcript	SO:0000185
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	SO	399284	SO:0000232	SO:0000483	snoRNA_primary_transcript	SO:0000185
2	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SO	399285	SO:0000233	SO:0000673	mature_transcript	SO:0000831
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SO	399286	SO:0000234	SO:0000233	mRNA	SO:0000673
2	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SOFA	protein_binding_site	SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	399287	SO:0000235	SO:0001654	TF_binding_site	SO:0000410
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	399288	SO:0000235	SO:0001679	TF_binding_site	SO:0005836
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	SO	399289	SO:0000236	SO:0000717	ORF	SO:0001410
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	399290	SO:0000237	SO:0000733	transcript_attribute	SO:0000400
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	399291	SO:0000238	SO:0000182	foldback_element	SO:0000101
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The sequences extending on either side of a specific region." [SO:ke]	SO	399292	SO:0000239	SO:0001412	flanking_region	SO:0000001
2	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	399293	SO:0000240	SO:0001507	chromosome_variation	SO:0001260
2	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"" []	SO	399294	SO:0000240	SO:0001524	chromosome_variation	SO:0001506
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	399295	SO:0000241	SO:0000203	internal_UTR	SO:0000836
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	399296	SO:0000242	SO:0000203	untranslated_region_polycistronic_mRNA	SO:0000836
2	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	five_prime_UTR	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	399297	SO:0000243	SO:0000139	internal_ribosome_entry_site	SO:0000204
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	399298	SO:0000243	SO:0000139	internal_ribosome_entry_site	SO:0000836
2	"" []	\N	transcript_attribute	\N	\N	sequence	"A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]	SO	399299	SO:0000246	SO:0000863	polyadenylated	SO:0000237
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"" []	SO	399300	SO:0000248	SO:1000002	sequence_length_variation	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	399301	SO:0000248	SO:1000002	sequence_length_variation	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post_transcriptionally modified base." [SO:ke]	SO	399302	SO:0000250	SO:0001236	modified_RNA_base_feature	SO:0001411
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SO	399303	SO:0000252	SO:0000655	rRNA	SO:0000233
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SO	399304	SO:0000253	SO:0000655	tRNA	SO:0000233
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	399305	SO:0000254	SO:0000253	alanyl_tRNA	SO:0000655
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	399306	SO:0000255	SO:0000209	rRNA_small_subunit_primary_transcript	SO:0000483
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	399307	SO:0000256	SO:0000253	asparaginyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	399308	SO:0000257	SO:0000253	aspartyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	399309	SO:0000258	SO:0000253	cysteinyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	399310	SO:0000259	SO:0000253	glutaminyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	399311	SO:0000260	SO:0000253	glutamyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	399312	SO:0000261	SO:0000253	glycyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	399313	SO:0000262	SO:0000253	histidyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	399314	SO:0000263	SO:0000253	isoleucyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	399315	SO:0000264	SO:0000253	leucyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	399316	SO:0000265	SO:0000253	lysyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	399317	SO:0000266	SO:0000253	methionyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	399318	SO:0000267	SO:0000253	phenylalanyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	399319	SO:0000268	SO:0000253	prolyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	399320	SO:0000269	SO:0000253	seryl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	399321	SO:0000270	SO:0000253	threonyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	399322	SO:0000271	SO:0000253	tryptophanyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	399323	SO:0000272	SO:0000253	tyrosyl_tRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	399324	SO:0000273	SO:0000253	valyl_tRNA	SO:0000655
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SO	399325	SO:0000274	SO:0000655	snRNA	SO:0000233
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SO	399326	SO:0000275	SO:0000655	snoRNA	SO:0000233
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	399327	SO:0000276	SO:0000370	miRNA	SO:0000655
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that is bound by another molecule." [SO:ke]	SO	399328	SO:0000277	SO:0000733	bound_by_factor	SO:0000400
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is bound by a nucleic acid." [SO:xp]	SO	399329	SO:0000278	SO:0000673	transcript_bound_by_nucleic_acid	SO:0000831
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is bound by a protein." [SO:xp]	SO	399330	SO:0000279	SO:0000673	transcript_bound_by_protein	SO:0000831
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is engineered." [SO:xp]	SO	399331	SO:0000280	SO:0000704	engineered_gene	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A gene that is engineered." [SO:xp]	SO	399332	SO:0000280	SO:0000804	engineered_gene	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A gene that is engineered." [SO:xp]	SO	399333	SO:0000280	SO:0000804	engineered_gene	SO:0001409
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	399334	SO:0000281	SO:0000280	engineered_foreign_gene	SO:0000704
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	399335	SO:0000281	SO:0000280	engineered_foreign_gene	SO:0000804
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	399336	SO:0000281	SO:0000285	engineered_foreign_gene	SO:0000704
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	399337	SO:0000281	SO:0000805	engineered_foreign_gene	SO:0000001
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	399338	SO:0000281	SO:0000805	engineered_foreign_gene	SO:0000804
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	399339	SO:0000282	SO:0000108	mRNA_with_minus_1_frameshift	SO:0000234
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	399340	SO:0000283	SO:0000111	engineered_foreign_transposable_element_gene	SO:0000101
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	399341	SO:0000283	SO:0000111	engineered_foreign_transposable_element_gene	SO:0000704
2	"A gene that is engineered." [SO:xp]	\N	engineered_gene	\N	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	399342	SO:0000283	SO:0000281	engineered_foreign_transposable_element_gene	SO:0000280
2	"A gene that is foreign." [SO:xp]	\N	foreign_gene	\N	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	399343	SO:0000283	SO:0000281	engineered_foreign_transposable_element_gene	SO:0000285
2	"A region that is engineered and foreign." [SO:xp]	\N	engineered_foreign_region	\N	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	399344	SO:0000283	SO:0000281	engineered_foreign_transposable_element_gene	SO:0000805
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is foreign." [SO:xp]	SO	399345	SO:0000285	SO:0000704	foreign_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399346	SO:0000286	SO:0000657	long_terminal_repeat	SO:0001411
2	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399347	SO:0000286	SO:0000186	long_terminal_repeat	SO:0000180
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is a fusion." [SO:xp]	SO	399348	SO:0000287	SO:0000704	fusion_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A fusion gene that is engineered." [SO:xp]	SO	399349	SO:0000288	SO:0000280	engineered_fusion_gene	SO:0000704
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A fusion gene that is engineered." [SO:xp]	SO	399350	SO:0000288	SO:0000280	engineered_fusion_gene	SO:0000804
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A fusion gene that is engineered." [SO:xp]	SO	399351	SO:0000288	SO:0000287	engineered_fusion_gene	SO:0000704
2	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SOFA	tandem_repeat	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	SO	399352	SO:0000289	SO:0000005	microsatellite	SO:0000705
2	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	satellite_DNA	SOFA	SOFA	sequence	"" []	SO	399353	SO:0000290	SO:0000289	dinucleotide_repeat_microsatellite_feature	SO:0000005
2	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	satellite_DNA	SOFA	SOFA	sequence	"" []	SO	399354	SO:0000291	SO:0000289	trinucleotide_repeat_microsatellite_feature	SO:0000005
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	399355	SO:0000293	SO:0000657	engineered_foreign_repetitive_element	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	399356	SO:0000293	SO:0000805	engineered_foreign_repetitive_element	SO:0000001
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	399357	SO:0000293	SO:0000805	engineered_foreign_repetitive_element	SO:0000804
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	SO	399358	SO:0000294	SO:0000657	inverted_repeat	SO:0001411
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	399359	SO:0000295	SO:0000662	U12_intron	SO:0000188
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732207	SO:0000296	SO:0001411	origin_of_replication	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399361	SO:0000296	SO:0001235	origin_of_replication	SO:0001411
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399362	SO:0000297	SO:0000296	D_loop	SO:0001235
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399363	SO:0000297	SO:0000296	D_loop	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	399364	SO:0000298	SO:0001411	recombination_feature	SO:0000001
2	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	399365	SO:0000299	SO:0000669	specific_recombination_site	SO:0000298
2	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	399366	SO:0000300	SO:0000299	recombination_feature_of_rearranged_gene	SO:0000669
2	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	399367	SO:0000301	SO:0000300	vertebrate_immune_system_gene_recombination_feature	SO:0000299
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399368	SO:0000302	SO:0000939	J_gene_recombination_feature	SO:0000301
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	399369	SO:0000303	SO:0000835	clip	SO:0000185
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	399370	SO:0000303	SO:0000835	clip	SO:0000833
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399371	SO:0000305	SO:0001236	modified_DNA_base	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399372	SO:0000305	SO:0001720	modified_DNA_base	SO:0001411
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SOFA	base	SOFA	SOFA	sequence	"A nucleotide modified by methylation." [SO:ke]	SO	399373	SO:0000306	SO:0000305	methylated_DNA_base_feature	SO:0001236
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SOFA	epigenetically_modified_region	SOFA	SOFA	sequence	"A nucleotide modified by methylation." [SO:ke]	SO	399374	SO:0000306	SO:0000305	methylated_DNA_base_feature	SO:0001720
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]	SO	399375	SO:0000307	SO:0001411	CpG_island	SO:0000001
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"Attribute to describe a feature that has been experimentally verified." [SO:ke]	SO	399376	SO:0000312	SO:0000789	experimentally_determined	SO:0000905
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399377	SO:0000313	SO:0000122	stem_loop	SO:0000002
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]	SO	399378	SO:0000314	SO:0000657	direct_repeat	SO:0001411
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	399379	SO:0000315	SO:0000835	TSS	SO:0000185
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	399380	SO:0000315	SO:0000835	TSS	SO:0000833
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	399381	SO:0000316	SO:0000836	CDS	SO:0000234
2	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	399382	SO:0000316	SO:0000836	CDS	SO:0000834
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	399383	SO:0000317	SO:0000151	cDNA_clone	SO:0000695
2	"A region of a CDS." [SO:cb]	SOFA	CDS_region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	399384	SO:0000318	SO:0000360	start_codon	SO:0000851
2	"A region of a CDS." [SO:cb]	SOFA	CDS_region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	399385	SO:0000319	SO:0000360	stop_codon	SO:0000851
2	"A regulatory_region that modulates splicing." [SO:ke]	\N	splicing_regulatory_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	399386	SO:0000320	SO:0000344	intronic_splice_enhancer	SO:0001056
2	"An intron which is spliced by the spliceosome." [SO:ke]	\N	spliceosomal_intron	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	399387	SO:0000320	SO:0000841	intronic_splice_enhancer	SO:0000662
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	399388	SO:0000320	SO:0000841	intronic_splice_enhancer	SO:0000835
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	399389	SO:0000321	SO:0000108	mRNA_with_plus_1_frameshift	SO:0000234
2	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	\N	nuclease_binding_site	SOFA	SOFA	sequence	"" []	SO	399390	SO:0000322	SO:0000684	nuclease_hypersensitive_site	SO:0000059
2	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	399391	SO:0000323	SO:0000851	coding_start	SO:0000316
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	399392	SO:0000323	SO:0000851	coding_start	SO:0000836
2	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SO	399393	SO:0000324	SO:0000696	tag	SO:0000695
2	"A primary transcript that is never translated into a protein." [SO:ke]	SOFA	nc_primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	399394	SO:0000325	SO:0000209	rRNA_large_subunit_primary_transcript	SO:0000483
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	SOFA	sequence	"A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	SO	399395	SO:0000326	SO:0000324	SAGE_tag	SO:0000696
2	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	399396	SO:0000327	SO:0000851	coding_end	SO:0000316
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	399397	SO:0000327	SO:0000851	coding_end	SO:0000836
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"" []	SO	399398	SO:0000328	SO:0000051	microarray_oligo	SO:0000696
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	399399	SO:0000329	SO:0000108	mRNA_with_plus_2_frameshift	SO:0000234
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	399400	SO:0000330	SO:0001410	conserved_region	SO:0000001
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	SOFA	sequence	"Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]	SO	399401	SO:0000331	SO:0000324	STS	SO:0000696
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"Coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	399402	SO:0000332	SO:0000330	coding_conserved_region	SO:0001410
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	399403	SO:0000333	SO:0000699	exon_junction	SO:0000110
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	399404	SO:0000333	SO:0000233	exon_junction	SO:0000673
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	399405	SO:0000334	SO:0000330	nc_conserved_region	SO:0001410
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	399406	SO:0000335	SO:0000108	mRNA_with_minus_2_frameshift	SO:0000234
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	399407	SO:0000336	SO:0001411	pseudogene	SO:0000001
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	SOFA	sequence	"A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]	SO	399408	SO:0000337	SO:0000442	RNAi_reagent	SO:0000696
2	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	399409	SO:0000338	SO:0000208	MITE	SO:0000182
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region in a genome which promotes recombination." [SO:rd]	SO	399410	SO:0000339	SO:0000298	recombination_hotspot	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SO	399411	SO:0000340	SO:0001235	chromosome	SO:0001411
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SOFA	chromosome	SOFA	SOFA	sequence	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SO	399412	SO:0000341	SO:0000830	chromosome_band	SO:0000340
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SO	399413	SO:0000341	SO:0000830	chromosome_band	SO:0001411
2	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	399414	SO:0000342	SO:0000299	site_specific_recombination_target_region	SO:0000669
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SO	399415	SO:0000343	SO:0001410	match	SO:0000001
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"Region of a transcript that regulates splicing." [SO:ke]	SO	399416	SO:0000344	SO:0001056	splice_enhancer	SO:0001679
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SOFA	oligo	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	SO	399417	SO:0000345	SO:0000324	EST	SO:0000696
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"" []	SO	399418	SO:0000346	SO:0000947	loxP_site	SO:0000342
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A match against a nucleotide sequence." [SO:ke]	SO	399419	SO:0000347	SO:0000343	nucleotide_match	SO:0001410
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	SO	399420	SO:0000348	SO:0000443	nucleic_acid	SO:0000400
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A match against a protein sequence." [SO:ke]	SO	399421	SO:0000349	SO:0000343	protein_match	SO:0001410
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	399422	SO:0000350	SO:0000948	FRT_site	SO:0000342
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]	SO	399423	SO:0000351	SO:0000443	synthetic_sequence	SO:0000400
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	SO	399424	SO:0000352	SO:0000348	DNA	SO:0000443
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SO	399425	SO:0000353	SO:0001248	sequence_assembly	SO:0001410
2	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	\N	nuclease_binding_site	SOFA	SOFA	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	399426	SO:0000354	SO:0000684	group_1_intron_homing_endonuclease_target_region	SO:0000059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]	SO	399427	SO:0000355	SO:0000298	haplotype_block	SO:0001411
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb]	SO	399428	SO:0000356	SO:0000348	RNA	SO:0000443
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]	SO	399429	SO:0000357	SO:0000733	flanked	SO:0000400
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]	SO	399430	SO:0000359	SO:0000357	floxed	SO:0000733
2	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SOFA	CDS	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	399431	SO:0000360	SO:0000851	codon	SO:0000316
2	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	399432	SO:0000360	SO:0000851	codon	SO:0000836
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]	SO	399433	SO:0000361	SO:0000357	FRT_flanked	SO:0000733
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]	SO	399434	SO:0000362	SO:0000790	invalidated_by_chimeric_cDNA	SO:0000905
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A transgene that is floxed." [SO:xp]	SO	399435	SO:0000363	SO:0000902	floxed_gene	SO:0000704
2	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	SOFA	sequence	"The region of sequence surrounding a transposable element." [SO:ke]	SO	399436	SO:0000364	SO:0000239	transposable_element_flanking_region	SO:0001412
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	SO	399437	SO:0000365	SO:0001039	integron	SO:0001037
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The junction where an insertion occurred." [SO:ke]	SO	399438	SO:0000366	SO:0000699	insertion_site	SO:0000110
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	399439	SO:0000367	SO:0000946	attI_site	SO:0000342
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	399440	SO:0000367	SO:0000365	attI_site	SO:0001039
2	"A sequence_feature with an extent of zero." [SO:ke]	SOFA	junction	SOFA	SOFA	sequence	"The junction in a genome where a transposable_element has inserted." [SO:ke]	SO	399441	SO:0000368	SO:0000366	transposable_element_insertion_site	SO:0000699
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SO	399442	SO:0000370	SO:0000655	small_regulatory_ncRNA	SO:0000233
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	399443	SO:0000371	SO:0000182	conjugative_transposon	SO:0000101
2	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	399444	SO:0000372	SO:0000673	enzymatic_RNA	SO:0000831
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A recombinationally rearranged gene by inversion." [SO:xp]	SO	399445	SO:0000373	SO:0000456	recombinationally_inverted_gene	SO:0000704
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"An RNA with catalytic activity." [SO:ma]	SO	399446	SO:0000374	SO:0000372	ribozyme	SO:0000673
2	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	399447	SO:0000375	SO:0000651	rRNA_5_8S	SO:0000252
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	399448	SO:0000376	SO:0000370	RNA_6S	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	399449	SO:0000377	SO:0000370	CsrB_RsmB_RNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	399450	SO:0000378	SO:0000370	DsrA_RNA	SO:0000655
2	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	399451	SO:0000379	SO:0000378	GcvB_RNA	SO:0000370
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	SOFA	nucleotide_motif	SOFA	SOFA	sequence	"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]	SO	399452	SO:0000380	SO:0000715	hammerhead_ribozyme	SO:0000714
2	"A self spliced intron." [SO:ke]	\N	autocatalytically_spliced_intron	SOFA	SOFA	sequence	"" []	SO	399453	SO:0000381	SO:0000603	group_IIA_intron	SO:0000588
2	"A self spliced intron." [SO:ke]	\N	autocatalytically_spliced_intron	SOFA	SOFA	sequence	"" []	SO	399454	SO:0000382	SO:0000603	group_IIB_intron	SO:0000588
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	399455	SO:0000383	SO:0000644	MicF_RNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	399456	SO:0000384	SO:0000370	OxyS_RNA	SO:0000655
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SO	399457	SO:0000385	SO:0000655	RNase_MRP_RNA	SO:0000233
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SO	399458	SO:0000386	SO:0000655	RNase_P_RNA	SO:0000233
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	399459	SO:0000387	SO:0000370	RprA_RNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	399460	SO:0000388	SO:0000370	RRE_RNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	399461	SO:0000389	SO:0000370	spot_42_RNA	SO:0000655
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SO	399462	SO:0000390	SO:0000655	telomerase_RNA	SO:0000233
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	399463	SO:0000391	SO:0000274	U1_snRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	399464	SO:0000392	SO:0000274	U2_snRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	399465	SO:0000393	SO:0000274	U4_snRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	399466	SO:0000394	SO:0000274	U4atac_snRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	399467	SO:0000395	SO:0000274	U5_snRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	399468	SO:0000396	SO:0000274	U6_snRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	399469	SO:0000397	SO:0000274	U6atac_snRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	399470	SO:0000398	SO:0000274	U11_snRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	399471	SO:0000399	SO:0000274	U12_snRNA	SO:0000655
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	399472	SO:0000401	SO:0000733	gene_attribute	SO:0000400
2	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SOFA	snoRNA	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	399473	SO:0000403	SO:0000593	U14_snoRNA	SO:0000275
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SO	399474	SO:0000404	SO:0000655	vault_RNA	SO:0000233
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SO	399475	SO:0000405	SO:0000655	Y_RNA	SO:0000233
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	399476	SO:0000406	SO:0000188	twintron	SO:0000835
2	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	399477	SO:0000407	SO:0000650	rRNA_18S	SO:0000252
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens,SOFA	region	SOFA	SOFA	sequence	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SO	399478	SO:0000409	SO:0001411	binding_site	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SO	399479	SO:0000410	SO:0000409	protein_binding_site	SO:0001411
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A region that rescues." [SO:xp]	SO	399480	SO:0000411	SO:0000695	rescue_region	SO:0001409
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]	SO	399481	SO:0000412	SO:0000143	restriction_fragment	SO:0001410
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A region where the sequence differs from that of a specified sequence." [SO:ke]	SO	399482	SO:0000413	SO:0000700	sequence_difference	SO:0001410
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]	SO	399483	SO:0000414	SO:0000790	invalidated_by_genomic_contamination	SO:0000905
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]	SO	399484	SO:0000415	SO:0000790	invalidated_by_genomic_polyA_primed_cDNA	SO:0000905
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]	SO	399485	SO:0000416	SO:0000790	invalidated_by_partial_processing	SO:0000905
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	399486	SO:0000417	SO:0001070	polypeptide_domain	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	399487	SO:0000417	SO:0100021	polypeptide_domain	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399488	SO:0000418	SO:0001527	signal_peptide	SO:0000839
2	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens,SOFA	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399489	SO:0000418	SO:0001062	signal_peptide	SO:0100011
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens,SOFA	polypeptide	SOFA	biosapiens,SOFA	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	732343	SO:0000419	SO:0000839	mature_protein_region	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	732344	SO:0000419	SO:0000839	mature_protein_region	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	399492	SO:0000419	SO:0001063	mature_protein_region	SO:0000839
2	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	\N	terminal_inverted_repeat_element	\N	\N	sequence	"" []	SO	399493	SO:0000420	SO:0000481	five_prime_terminal_inverted_repeat	SO:0000208
2	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	\N	inverted_repeat	SOFA	\N	sequence	"" []	SO	399494	SO:0000420	SO:0000481	five_prime_terminal_inverted_repeat	SO:0000294
2	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	\N	terminal_inverted_repeat_element	\N	\N	sequence	"" []	SO	399495	SO:0000421	SO:0000481	three_prime_terminal_inverted_repeat	SO:0000208
2	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	\N	inverted_repeat	SOFA	\N	sequence	"" []	SO	399496	SO:0000421	SO:0000481	three_prime_terminal_inverted_repeat	SO:0000294
2	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	399497	SO:0000422	SO:0000848	U5_LTR_region	SO:0000286
2	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	399498	SO:0000422	SO:0000848	U5_LTR_region	SO:0000840
2	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	399499	SO:0000423	SO:0000848	R_LTR_region	SO:0000286
2	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	399500	SO:0000423	SO:0000848	R_LTR_region	SO:0000840
2	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	399501	SO:0000424	SO:0000848	U3_LTR_region	SO:0000286
2	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	399502	SO:0000424	SO:0000848	U3_LTR_region	SO:0000840
2	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	399503	SO:0000425	SO:0000286	five_prime_LTR	SO:0000186
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	399504	SO:0000425	SO:0000286	five_prime_LTR	SO:0000657
2	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	399505	SO:0000426	SO:0000286	three_prime_LTR	SO:0000186
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	399506	SO:0000426	SO:0000286	three_prime_LTR	SO:0000657
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399507	SO:0000427	SO:0000423	R_five_prime_LTR_region	SO:0000848
2	"" []	\N	five_prime_LTR	\N	\N	sequence	"" []	SO	399508	SO:0000427	SO:0000850	R_five_prime_LTR_region	SO:0000425
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399509	SO:0000427	SO:0000850	R_five_prime_LTR_region	SO:0000848
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399510	SO:0000428	SO:0000422	U5_five_prime_LTR_region	SO:0000848
2	"" []	\N	five_prime_LTR	\N	\N	sequence	"" []	SO	399511	SO:0000428	SO:0000850	U5_five_prime_LTR_region	SO:0000425
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399512	SO:0000428	SO:0000850	U5_five_prime_LTR_region	SO:0000848
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399513	SO:0000429	SO:0000424	U3_five_prime_LTR_region	SO:0000848
2	"" []	\N	five_prime_LTR	\N	\N	sequence	"" []	SO	399514	SO:0000429	SO:0000850	U3_five_prime_LTR_region	SO:0000425
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399515	SO:0000429	SO:0000850	U3_five_prime_LTR_region	SO:0000848
2	"" []	\N	three_prime_LTR	\N	\N	sequence	"" []	SO	399516	SO:0000430	SO:0000849	R_three_prime_LTR_region	SO:0000426
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399517	SO:0000430	SO:0000849	R_three_prime_LTR_region	SO:0000848
2	"" []	\N	three_prime_LTR	\N	\N	sequence	"" []	SO	399518	SO:0000431	SO:0000849	U3_three_prime_LTR_region	SO:0000426
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399519	SO:0000431	SO:0000849	U3_three_prime_LTR_region	SO:0000848
2	"" []	\N	three_prime_LTR	\N	\N	sequence	"" []	SO	399520	SO:0000432	SO:0000849	U5_three_prime_LTR_region	SO:0000426
2	"" []	\N	LTR_component	\N	\N	sequence	"" []	SO	399521	SO:0000432	SO:0000849	U5_three_prime_LTR_region	SO:0000848
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	399522	SO:0000433	SO:0000657	non_LTR_retrotransposon_polymeric_tract	SO:0001411
2	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	399523	SO:0000433	SO:0000840	non_LTR_retrotransposon_polymeric_tract	SO:0001412
2	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	399524	SO:0000433	SO:0000189	non_LTR_retrotransposon_polymeric_tract	SO:0000180
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]	SO	399525	SO:0000434	SO:0000314	target_site_duplication	SO:0000657
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	399526	SO:0000435	SO:0000330	RR_tract	SO:0001410
2	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	399527	SO:0000435	SO:0000186	RR_tract	SO:0000180
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	SO	399528	SO:0000436	SO:0000296	ARS	SO:0001235
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	SO	399529	SO:0000436	SO:0000296	ARS	SO:0001411
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"" []	SO	399530	SO:0000439	SO:1000030	inverted_ring_chromosome	SO:1000028
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"" []	SO	399531	SO:0000439	SO:1000045	inverted_ring_chromosome	SO:1000028
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	399532	SO:0000440	SO:0001235	vector_replicon	SO:0001411
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	399533	SO:0000440	SO:0000151	vector_replicon	SO:0000695
2	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A single stranded oligonucleotide." [SO:ke]	SO	399534	SO:0000441	SO:0000696	ss_oligo	SO:0000695
2	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A double stranded oligonucleotide." [SO:ke]	SO	399535	SO:0000442	SO:0000696	ds_oligo	SO:0000695
2	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	\N	exon	SOFA	SOFA	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	399536	SO:0000444	SO:0000198	three_prime_noncoding_exon	SO:0000147
2	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	\N	exon	SOFA	SOFA	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	399537	SO:0000445	SO:0000198	five_prime_noncoding_exon	SO:0000147
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	399538	SO:0000446	SO:0000188	UTR_intron	SO:0000835
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	399539	SO:0000447	SO:0000446	five_prime_UTR_intron	SO:0000188
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	399540	SO:0000448	SO:0000446	three_prime_UTR_intron	SO:0000188
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"A sequence of nucleotides or amino acids which, by design, has a \\"random\\" order of components, given a predetermined input frequency of these components." [SO:ma]	SO	399541	SO:0000449	SO:0000351	random_sequence	SO:0000443
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	SO	399542	SO:0000450	SO:0000830	interband	SO:0000340
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	SO	399543	SO:0000450	SO:0000830	interband	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes a polyadenylated mRNA." [SO:xp]	SO	399544	SO:0000451	SO:0001217	gene_with_polyadenylated_mRNA	SO:0000704
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	399545	SO:0000453	SO:1000183	chromosomal_transposition	SO:0000240
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SO	399546	SO:0000454	SO:0000655	rasiRNA	SO:0000233
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes an mRNA with a frameshift." [SO:xp]	SO	399547	SO:0000455	SO:0001217	gene_with_mRNA_with_frameshift	SO:0000704
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is recombinationally rearranged." [SO:ke]	SO	399548	SO:0000456	SO:0000704	recombinationally_rearranged_gene	SO:0001411
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	399549	SO:0000457	SO:1000037	interchromosomal_duplication	SO:1000183
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399550	SO:0000458	SO:0000460	D_gene_segment	SO:0000301
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene with a transcript that is trans-spliced." [SO:xp]	SO	399551	SO:0000459	SO:0000704	gene_with_trans_spliced_transcript	SO:0001411
2	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	399552	SO:0000460	SO:0000301	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000300
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	399553	SO:0000461	SO:1000029	inversion_derived_bipartite_deficiency	SO:1000028
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A non-functional descendant of a functional entity." [SO:cjm]	SO	399554	SO:0000462	SO:0001411	pseudogenic_region	SO:0000001
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A gene that encodes more than one transcript." [SO:ke]	SO	399555	SO:0000463	SO:0000401	encodes_alternately_spliced_transcripts	SO:0000733
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A non-functional descendant of an exon." [SO:ke]	SO	399556	SO:0000464	SO:0000462	decayed_exon	SO:0001411
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	399557	SO:0000465	SO:1000029	inversion_derived_deficiency_plus_duplication	SO:1000028
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	399558	SO:0000465	SO:1000038	inversion_derived_deficiency_plus_duplication	SO:1000028
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	399559	SO:0000465	SO:1000038	inversion_derived_deficiency_plus_duplication	SO:1000037
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399560	SO:0000466	SO:0000460	V_gene_segment	SO:0000301
2	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]	SO	399561	SO:0000467	SO:0000130	post_translationally_regulated_by_protein_stability	SO:0000119
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	399562	SO:0000468	SO:0000143	golden_path_fragment	SO:0001410
2	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	399563	SO:0000468	SO:0000688	golden_path_fragment	SO:0000353
2	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]	SO	399564	SO:0000469	SO:0000130	post_translationally_regulated_by_protein_modification	SO:0000119
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399565	SO:0000470	SO:0000460	J_gene_segment	SO:0000301
2	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation." [SO:ke]	SO	399566	SO:0000471	SO:0000123	autoregulated	SO:0000119
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	SO	399567	SO:0000472	SO:0000353	tiling_path	SO:0001248
2	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	399568	SO:0000473	SO:0000126	negatively_autoregulated	SO:0000123
2	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	399569	SO:0000473	SO:0000471	negatively_autoregulated	SO:0000123
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	399570	SO:0000474	SO:0000143	tiling_path_fragment	SO:0001410
2	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	SOFA	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	399571	SO:0000474	SO:0000472	tiling_path_fragment	SO:0000353
2	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	399572	SO:0000475	SO:0000125	positively_autoregulated	SO:0000123
2	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	399573	SO:0000475	SO:0000471	positively_autoregulated	SO:0000123
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	399574	SO:0000476	SO:0000150	contig_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	399575	SO:0000476	SO:0000150	contig_read	SO:0000149
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399576	SO:0000478	SO:0000460	C_gene_segment	SO:0000301
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is trans-spliced." [SO:xp]	SO	399577	SO:0000479	SO:0000673	trans_spliced_transcript	SO:0000831
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	399578	SO:0000480	SO:0000151	tiling_path_clone	SO:0000695
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	399579	SO:0000480	SO:0000474	tiling_path_clone	SO:0000143
2	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	\N	tiling_path	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	399580	SO:0000480	SO:0000474	tiling_path_clone	SO:0000472
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	399581	SO:0000481	SO:0000294	terminal_inverted_repeat	SO:0000657
2	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	399582	SO:0000481	SO:0000208	terminal_inverted_repeat	SO:0000182
2	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	399583	SO:0000482	SO:0000301	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000300
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A primary transcript that is never translated into a protein." [SO:ke]	SO	399584	SO:0000483	SO:0000185	nc_primary_transcript	SO:0000673
2	"A region of an exon." [RSC:cb]	SOFA	exon_region	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	399585	SO:0000484	SO:0001214	three_prime_coding_exon_noncoding_region	SO:0000852
2	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SOFA	coding_exon	SOFA	\N	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	399586	SO:0000484	SO:0000202	three_prime_coding_exon_noncoding_region	SO:0000195
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399587	SO:0000485	SO:0000938	DJ_J_cluster	SO:0000301
2	"A region of an exon." [RSC:cb]	SOFA	exon_region	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	399588	SO:0000486	SO:0001214	five_prime_coding_exon_noncoding_region	SO:0000852
2	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SOFA	coding_exon	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	399589	SO:0000486	SO:0000200	five_prime_coding_exon_noncoding_region	SO:0000195
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399590	SO:0000487	SO:0000938	VDJ_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399591	SO:0000488	SO:0000938	VDJ_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399592	SO:0000489	SO:0000938	VJ_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399593	SO:0000490	SO:0000938	VJ_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399594	SO:0000491	SO:0000938	VJ_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	399595	SO:0000492	SO:0000939	D_gene_recombination_feature	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399596	SO:0000493	SO:0000561	three_prime_D_heptamer	SO:0000939
2	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399597	SO:0000493	SO:0000570	three_prime_D_heptamer	SO:0000492
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399598	SO:0000494	SO:0000562	three_prime_D_nonamer	SO:0000939
2	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399599	SO:0000494	SO:0000570	three_prime_D_nonamer	SO:0000492
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399600	SO:0000495	SO:0000563	three_prime_D_spacer	SO:0000301
2	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399601	SO:0000495	SO:0000570	three_prime_D_spacer	SO:0000492
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399602	SO:0000496	SO:0000561	five_prime_D_heptamer	SO:0000939
2	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399603	SO:0000496	SO:0000556	five_prime_D_heptamer	SO:0000492
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399604	SO:0000497	SO:0000562	five_prime_D_nonamer	SO:0000939
2	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399605	SO:0000497	SO:0000556	five_prime_D_nonamer	SO:0000492
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399606	SO:0000498	SO:0000563	five_prime_D_spacer	SO:0000301
2	"" []	\N	D_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399607	SO:0000498	SO:0000556	five_prime_D_spacer	SO:0000492
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]	SO	399608	SO:0000499	SO:0000353	virtual_sequence	SO:0001248
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]	SO	399609	SO:0000500	SO:0000028	Hoogsteen_base_pair	SO:0000002
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A type of non-canonical base-pairing." [SO:ke]	SO	399610	SO:0000501	SO:0000028	reverse_Hoogsteen_base_pair	SO:0000002
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399611	SO:0000504	SO:0000938	D_DJ_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399612	SO:0000505	SO:0000938	D_DJ_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399613	SO:0000506	SO:0000938	D_DJ_J_C_cluster	SO:0000301
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	732476	SO:0000507	SO:0000462	pseudogenic_exon	SO:0001411
2	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	399615	SO:0000507	SO:0000516	pseudogenic_exon	SO:0000336
2	"A non-functional descendant of a functional entity." [SO:cjm]	\N	pseudogenic_region	SOFA	\N	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	399616	SO:0000507	SO:0000516	pseudogenic_exon	SO:0000462
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399617	SO:0000508	SO:0000938	D_DJ_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399618	SO:0000509	SO:0000482	D_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399619	SO:0000510	SO:0000936	VD_gene_segment	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399620	SO:0000511	SO:0000482	J_C_cluster	SO:0000301
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	399621	SO:0000512	SO:1000029	inversion_derived_deficiency_plus_aneuploid	SO:1000028
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399622	SO:0000513	SO:0000482	J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399623	SO:0000514	SO:0000562	J_nonamer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399624	SO:0000514	SO:0000302	J_nonamer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399625	SO:0000515	SO:0000561	J_heptamer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399626	SO:0000515	SO:0000302	J_heptamer	SO:0000939
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	SO	399627	SO:0000516	SO:0000462	pseudogenic_transcript	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	SO	399628	SO:0000516	SO:0000336	pseudogenic_transcript	SO:0001411
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399629	SO:0000517	SO:0000563	J_spacer	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399630	SO:0000517	SO:0000302	J_spacer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399631	SO:0000518	SO:0000938	V_DJ_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399632	SO:0000519	SO:0000938	V_DJ_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399633	SO:0000520	SO:0000938	V_VDJ_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399634	SO:0000521	SO:0000938	V_VDJ_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399635	SO:0000522	SO:0000938	V_VDJ_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399636	SO:0000523	SO:0000938	V_VJ_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399637	SO:0000524	SO:0000938	V_VJ_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399638	SO:0000525	SO:0000938	V_VJ_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399639	SO:0000526	SO:0000482	V_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399640	SO:0000527	SO:0000938	V_D_DJ_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399641	SO:0000528	SO:0000938	V_D_DJ_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399642	SO:0000529	SO:0000938	V_D_DJ_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399643	SO:0000530	SO:0000938	V_D_DJ_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399644	SO:0000531	SO:0000938	V_D_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399645	SO:0000532	SO:0000938	V_D_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399646	SO:0000533	SO:0000561	V_heptamer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399647	SO:0000533	SO:0000538	V_heptamer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399648	SO:0000534	SO:0000482	V_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399649	SO:0000535	SO:0000482	V_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399650	SO:0000536	SO:0000562	V_nonamer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399651	SO:0000536	SO:0000538	V_nonamer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399652	SO:0000537	SO:0000563	V_spacer	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399653	SO:0000537	SO:0000538	V_spacer	SO:0000939
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399654	SO:0000538	SO:0000939	V_gene_recombination_feature	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399655	SO:0000539	SO:0000938	DJ_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399656	SO:0000540	SO:0000938	DJ_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399657	SO:0000541	SO:0000938	VDJ_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399658	SO:0000542	SO:0000938	V_DJ_C_cluster	SO:0000301
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	399659	SO:0000544	SO:0000182	helitron	SO:0000101
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	399660	SO:0000545	SO:0000591	recoding_pseudoknot	SO:0000002
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	399661	SO:0000545	SO:1001268	recoding_pseudoknot	SO:0000836
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"" []	SO	399662	SO:0000546	SO:0000351	designed_sequence	SO:0000443
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	399663	SO:0000547	SO:1000038	inversion_derived_bipartite_duplication	SO:1000028
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	399664	SO:0000547	SO:1000038	inversion_derived_bipartite_duplication	SO:1000037
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes a transcript that is edited." [SO:xp]	SO	399665	SO:0000548	SO:0001217	gene_with_edited_transcript	SO:0000704
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	399666	SO:0000549	SO:1000038	inversion_derived_duplication_plus_aneuploid	SO:1000028
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	399667	SO:0000549	SO:1000038	inversion_derived_duplication_plus_aneuploid	SO:1000037
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	399668	SO:0000550	SO:1000183	aneuploid_chromosome	SO:0000240
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399669	SO:0000551	SO:0001679	polyA_signal_sequence	SO:0005836
2	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	five_prime_UTR	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	399670	SO:0000552	SO:0000139	Shine_Dalgarno_sequence	SO:0000204
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	399671	SO:0000552	SO:0000139	Shine_Dalgarno_sequence	SO:0000836
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399672	SO:0000553	SO:0000699	polyA_site	SO:0000110
2	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SOFA	UTR	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399673	SO:0000553	SO:0000205	polyA_site	SO:0000203
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081315	SO:0000553	SO:0000233	polyA_site	SO:0000673
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399675	SO:0000555	SO:0000303	five_prime_clip	SO:0000835
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399676	SO:0000556	SO:0000492	five_prime_D_recombination_signal_sequence	SO:0000939
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399677	SO:0000557	SO:0000303	three_prime_clip	SO:0000835
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399678	SO:0000558	SO:0000482	C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399679	SO:0000559	SO:0000482	D_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399680	SO:0000560	SO:0000482	D_J_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399681	SO:0000561	SO:0000939	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"" []	SO	399682	SO:0000562	SO:0000939	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000301
2	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	399683	SO:0000563	SO:0000301	vertebrate_immune_system_gene_recombination_spacer	SO:0000300
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399684	SO:0000564	SO:0000938	V_DJ_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399685	SO:0000565	SO:0000938	V_VDJ_J_C_cluster	SO:0000301
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399686	SO:0000566	SO:0000938	V_VJ_J_C_cluster	SO:0000301
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	399687	SO:0000567	SO:0000550	inversion_derived_aneuploid_chromosome	SO:1000183
2	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"" []	SO	399688	SO:0000568	SO:0000167	bidirectional_promoter	SO:0001055
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke]	SO	399689	SO:0000569	SO:0000733	retrotransposed	SO:0000400
2	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399690	SO:0000570	SO:0000492	three_prime_D_recombination_signal_sequence	SO:0000939
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399691	SO:0000571	SO:0000011	miRNA_encoding	SO:0000401
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399692	SO:0000572	SO:0000936	DJ_gene_segment	SO:0000301
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399693	SO:0000573	SO:0000011	rRNA_encoding	SO:0000401
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399694	SO:0000574	SO:0000936	VDJ_gene_segment	SO:0000301
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399695	SO:0000575	SO:0000011	scRNA_encoding	SO:0000401
2	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	399696	SO:0000576	SO:0000936	VJ_gene_segment	SO:0000301
2	"A region of a chromosome." [SO:ke]	SOFA	chromosome_part	SOFA	SOFA	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	399697	SO:0000577	SO:0000628	centromere	SO:0000830
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399698	SO:0000578	SO:0000011	snoRNA_encoding	SO:0000401
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A locatable feature on a transcript that is edited." [SO:ma]	SO	399699	SO:0000579	SO:0000833	edited_transcript_feature	SO:0000673
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A locatable feature on a transcript that is edited." [SO:ma]	SO	399700	SO:0000579	SO:0000833	edited_transcript_feature	SO:0001411
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	399701	SO:0000580	SO:0000232	methylation_guide_snoRNA_primary_transcript	SO:0000483
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	399702	SO:0000581	SO:0001411	cap	SO:0000001
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	399703	SO:0000582	SO:0000232	rRNA_cleavage_snoRNA_primary_transcript	SO:0000483
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	\N	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	399704	SO:0000583	SO:0000579	pre_edited_region	SO:0000833
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	399705	SO:0000584	SO:0000370	tmRNA	SO:0000655
2	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	399706	SO:0000585	SO:0000578	C_D_box_snoRNA_encoding	SO:0000011
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	SO	399707	SO:0000586	SO:0000483	tmRNA_primary_transcript	SO:0000185
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	intron	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	399708	SO:0000587	SO:0000588	group_I_intron	SO:0000188
2	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	399709	SO:0000588	SO:0000188	autocatalytically_spliced_intron	SO:0000835
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	SO	399710	SO:0000589	SO:0000483	SRP_RNA_primary_transcript	SO:0000185
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SO	399711	SO:0000590	SO:0000655	SRP_RNA	SO:0000233
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]	SO	399712	SO:0000591	SO:0000002	pseudoknot	SO:0001411
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]	SO	399713	SO:0000592	SO:0000591	H_pseudoknot	SO:0000002
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	399714	SO:0000593	SO:0000275	C_D_box_snoRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	399715	SO:0000594	SO:0000275	H_ACA_box_snoRNA	SO:0000655
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	399716	SO:0000595	SO:0000232	C_D_box_snoRNA_primary_transcript	SO:0000483
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	399717	SO:0000596	SO:0000232	H_ACA_box_snoRNA_primary_transcript	SO:0000483
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SO	399718	SO:0000602	SO:0000655	guide_RNA	SO:0000233
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	intron	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	399719	SO:0000603	SO:0000588	group_II_intron	SO:0000188
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	\N	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	399720	SO:0000604	SO:0000579	editing_block	SO:0000833
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]	SO	399721	SO:0000605	SO:0001411	intergenic_region	SO:0000001
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	\N	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	399722	SO:0000606	SO:0000579	editing_domain	SO:0000833
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	\N	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	399723	SO:0000607	SO:0000579	unedited_region	SO:0000833
2	"" []	\N	non_protein_coding	\N	\N	sequence	"" []	SO	399724	SO:0000608	SO:0000578	H_ACA_box_snoRNA_encoding	SO:0000011
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]	SO	399725	SO:0000609	SO:0001411	oligo_U_tail	SO:0000001
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]	SO	399726	SO:0000610	SO:0001411	polyA_sequence	SO:0000001
2	"An intron which is spliced by the spliceosome." [SO:ke]	SOFA	spliceosomal_intron	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	399727	SO:0000611	SO:0000841	branch_site	SO:0000662
2	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	399728	SO:0000611	SO:0000841	branch_site	SO:0000835
2	"An intron which is spliced by the spliceosome." [SO:ke]	SOFA	spliceosomal_intron	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	399729	SO:0000612	SO:0000841	polypyrimidine_tract	SO:0000662
2	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	399730	SO:0000612	SO:0000841	polypyrimidine_tract	SO:0000835
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	399731	SO:0000613	SO:0000752	bacterial_RNApol_promoter	SO:0001679
2	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	399732	SO:0000613	SO:0001203	bacterial_RNApol_promoter	SO:0000167
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	399733	SO:0000614	SO:0000141	bacterial_terminator	SO:0000673
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	399734	SO:0000614	SO:0000141	bacterial_terminator	SO:0001679
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	399735	SO:0000614	SO:0000752	bacterial_terminator	SO:0001679
2	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	terminator	SOFA	\N	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	399736	SO:0000615	SO:0000951	terminator_of_type_2_RNApol_III_promoter	SO:0000141
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	399737	SO:0000616	SO:0000835	transcription_end_site	SO:0000185
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	399738	SO:0000616	SO:0000835	transcription_end_site	SO:0000833
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"" []	SO	399739	SO:0000617	SO:0000171	RNApol_III_promoter_type_1	SO:0001203
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"" []	SO	399740	SO:0000618	SO:0000171	RNApol_III_promoter_type_2	SO:0001203
2	"" []	\N	promoter_element	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	399741	SO:0000619	SO:0001660	A_box	SO:0001659
2	"" []	\N	promoter_element	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	399742	SO:0000620	SO:0001660	B_box	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	399743	SO:0000620	SO:0000618	B_box	SO:0000171
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"" []	SO	399744	SO:0000621	SO:0000171	RNApol_III_promoter_type_3	SO:0001203
2	"" []	\N	promoter_element	\N	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	399745	SO:0000622	SO:0001660	C_box	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	399746	SO:0000622	SO:0000617	C_box	SO:0000171
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399747	SO:0000623	SO:0000011	snRNA_encoding	SO:0000401
2	"A region of a chromosome." [SO:ke]	SOFA	chromosome_part	SOFA	SOFA	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	399748	SO:0000624	SO:0000628	telomere	SO:0000830
2	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SOFA	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	399749	SO:0000625	SO:0000727	silencer	SO:0001055
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"" []	SO	399750	SO:0000626	SO:0000830	chromosomal_regulatory_element	SO:0000340
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	399751	SO:0000626	SO:0000830	chromosomal_regulatory_element	SO:0001411
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SO	399752	SO:0000627	SO:0001055	insulator	SO:0001679
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SOFA	chromosome	SOFA	SOFA	sequence	"" []	SO	399753	SO:0000628	SO:0000830	chromosomal_structural_element	SO:0000340
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"" []	SO	399754	SO:0000628	SO:0000830	chromosomal_structural_element	SO:0001411
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"" []	SO	1165525	SO:0000629	SO:0000836	five_prime_open_reading_frame	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"" []	SO	1165526	SO:0000629	SO:0000836	five_prime_open_reading_frame	SO:0000834
2	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	SOFA	sequence	"" []	SO	399757	SO:0000629	SO:0000204	five_prime_open_reading_frame	SO:0000203
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	399758	SO:0000630	SO:0000837	upstream_AUG_codon	SO:0000836
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	399759	SO:0000630	SO:0000203	upstream_AUG_codon	SO:0000836
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	399760	SO:0000631	SO:0000078	polycistronic_primary_transcript	SO:0000673
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	399761	SO:0000631	SO:0000185	polycistronic_primary_transcript	SO:0000673
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	399762	SO:0000632	SO:0000185	monocistronic_primary_transcript	SO:0000673
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	399763	SO:0000632	SO:0000665	monocistronic_primary_transcript	SO:0000673
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	399764	SO:0000633	SO:0000234	monocistronic_mRNA	SO:0000233
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	399765	SO:0000633	SO:0000665	monocistronic_mRNA	SO:0000673
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	399766	SO:0000634	SO:0000078	polycistronic_mRNA	SO:0000673
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	399767	SO:0000634	SO:0000234	polycistronic_mRNA	SO:0000233
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	SO	399768	SO:0000635	SO:0000185	mini_exon_donor_RNA	SO:0000673
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	399769	SO:0000636	SO:0000835	spliced_leader_RNA	SO:0000185
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	399770	SO:0000636	SO:0000835	spliced_leader_RNA	SO:0000833
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"" []	SO	399771	SO:0000636	SO:0000635	spliced_leader_RNA	SO:0000185
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A plasmid that is engineered." [SO:xp]	SO	399772	SO:0000637	SO:0000155	engineered_plasmid	SO:0001235
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A plasmid that is engineered." [SO:xp]	SO	399773	SO:0000637	SO:0000804	engineered_plasmid	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A plasmid that is engineered." [SO:xp]	SO	399774	SO:0000637	SO:0000804	engineered_plasmid	SO:0001409
2	"A primary transcript encoding a ribosomal RNA." [SO:ke]	\N	rRNA_primary_transcript	SOFA	\N	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	399775	SO:0000638	SO:0000838	transcribed_spacer_region	SO:0000209
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	399776	SO:0000638	SO:0000838	transcribed_spacer_region	SO:0000835
2	"A region of an rRNA primary transcript." [SO:ke]	\N	rRNA_primary_transcript_region	\N	\N	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	399777	SO:0000639	SO:0000638	internal_transcribed_spacer_region	SO:0000838
2	"A region of an rRNA primary transcript." [SO:ke]	\N	rRNA_primary_transcript_region	\N	\N	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	399778	SO:0000640	SO:0000638	external_transcribed_spacer_region	SO:0000838
2	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	satellite_DNA	SOFA	SOFA	sequence	"" []	SO	399779	SO:0000641	SO:0000289	tetranucleotide_repeat_microsatellite_feature	SO:0000005
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399780	SO:0000642	SO:0000011	SRP_RNA_encoding	SO:0000401
2	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SOFA	tandem_repeat	SOFA	SOFA	sequence	"A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]	SO	399781	SO:0000643	SO:0000005	minisatellite	SO:0000705
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SO	399782	SO:0000644	SO:0000655	antisense_RNA	SO:0000233
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The reverse complement of the primary transcript." [SO:ke]	SO	399783	SO:0000645	SO:0000185	antisense_primary_transcript	SO:0000673
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SO	399784	SO:0000646	SO:0000655	siRNA	SO:0000233
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a micro RNA." [SO:ke]	SO	399785	SO:0000647	SO:0000483	miRNA_primary_transcript	SO:0000185
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	399786	SO:0000648	SO:0000647	stRNA_primary_transcript	SO:0000483
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SO	399787	SO:0000649	SO:0000655	stRNA	SO:0000233
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	399788	SO:0000650	SO:0000252	small_subunit_rRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	399789	SO:0000651	SO:0000252	large_subunit_rRNA	SO:0000655
2	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	399790	SO:0000652	SO:0000651	rRNA_5S	SO:0000252
2	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	399791	SO:0000653	SO:0000651	rRNA_28S	SO:0000252
2	"A gene located in mitochondrial sequence." [SO:xp]	\N	mt_gene	\N	\N	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	399792	SO:0000654	SO:0000089	maxicircle_gene	SO:0000088
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	399793	SO:0000654	SO:0000742	maxicircle_gene	SO:0001235
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SO	399794	SO:0000655	SO:0000233	ncRNA	SO:0000673
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399795	SO:0000656	SO:0000011	stRNA_encoding	SO:0000401
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of sequence containing one or more repeat units." [SO:ke]	SO	399796	SO:0000657	SO:0001411	repeat_region	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A repeat that is located at dispersed sites in the genome." [SO:ke]	SO	399797	SO:0000658	SO:0000657	dispersed_repeat	SO:0001411
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399798	SO:0000659	SO:0000011	tmRNA_encoding	SO:0000401
2	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	399799	SO:0000662	SO:0000188	spliceosomal_intron	SO:0000835
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	399800	SO:0000663	SO:0000011	tRNA_encoding	SO:0000401
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"" []	SO	399801	SO:0000664	SO:0000830	introgressed_chromosome_region	SO:0000340
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	399802	SO:0000664	SO:0000830	introgressed_chromosome_region	SO:0001411
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is monocistronic." [SO:xp]	SO	399803	SO:0000665	SO:0000673	monocistronic_transcript	SO:0000831
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	399804	SO:0000666	SO:0000188	mobile_intron	SO:0000835
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	399805	SO:0000666	SO:0001037	mobile_intron	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	399806	SO:0000666	SO:0001037	mobile_intron	SO:0001411
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR,SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	SO	399807	SO:0000667	SO:0001059	insertion	SO:0000110
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	DBVAR,SOFA	region	SOFA	SOFA	sequence	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	SO	399808	SO:0000667	SO:0001411	insertion	SO:0000001
2	"A match against a nucleotide sequence." [SO:ke]	SOFA	nucleotide_match	SOFA	SOFA	sequence	"A match against an EST sequence." [SO:ke]	SO	399809	SO:0000668	SO:0000102	EST_match	SO:0000347
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	399810	SO:0000669	SO:0000298	sequence_rearrangement_feature	SO:0001411
2	"" []	\N	recombination_feature	\N	\N	sequence	"A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]	SO	399811	SO:0000670	SO:0000669	chromosome_breakage_sequence	SO:0000298
2	"" []	\N	recombination_feature	\N	\N	sequence	"A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]	SO	399812	SO:0000671	SO:0000669	internal_eliminated_sequence	SO:0000298
2	"" []	\N	recombination_feature	\N	\N	sequence	"A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]	SO	399813	SO:0000672	SO:0000669	macronucleus_destined_segment	SO:0000298
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SO	399814	SO:0000673	SO:0000831	transcript	SO:0001411
2	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	\N	cis_splice_site	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	399815	SO:0000676	SO:0000164	canonical_three_prime_splice_site	SO:0001419
2	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	\N	cis_splice_site	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	399816	SO:0000677	SO:0000163	canonical_five_prime_splice_site	SO:0001419
2	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	\N	cis_splice_site	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	399817	SO:0000678	SO:0000164	non_canonical_three_prime_splice_site	SO:0001419
2	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	\N	cis_splice_site	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	399818	SO:0000679	SO:0000163	non_canonical_five_prime_splice_site	SO:0001419
2	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	\N	codon	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	399819	SO:0000680	SO:0000318	non_canonical_start_codon	SO:0000360
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons." [SO:ke]	SO	399820	SO:0000681	SO:0000673	aberrant_processed_transcript	SO:0000831
2	"A regulatory_region that modulates splicing." [SO:ke]	\N	splicing_regulatory_region	SOFA	SOFA	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	399821	SO:0000683	SO:0000344	exonic_splice_enhancer	SO:0001056
2	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SOFA	nucleotide_to_protein_binding_site	SOFA	SOFA	sequence	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SO	399822	SO:0000684	SO:0000059	nuclease_sensitive_site	SO:0001654
2	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	\N	nuclease_sensitive_site	SOFA	\N	sequence	"" []	SO	399823	SO:0000685	SO:0000322	DNAseI_hypersensitive_site	SO:0000684
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	399824	SO:0000686	SO:1000044	translocation_element	SO:1000031
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]	SO	399825	SO:0000687	SO:0000699	deletion_junction	SO:0000110
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]	SO	399826	SO:0000688	SO:0000353	golden_path	SO:0001248
2	"A match against a nucleotide sequence." [SO:ke]	SOFA	nucleotide_match	SOFA	SOFA	sequence	"A match against cDNA sequence." [SO:ke]	SO	399827	SO:0000689	SO:0000102	cDNA_match	SO:0000347
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes a polycistronic transcript." [SO:xp]	SO	399828	SO:0000690	SO:0000704	gene_with_polycistronic_transcript	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	399829	SO:0000691	SO:0100011	cleaved_initiator_methionine	SO:0000839
2	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	399830	SO:0000691	SO:0100011	cleaved_initiator_methionine	SO:0001063
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes a dicistronic transcript." [SO:xp]	SO	399831	SO:0000692	SO:0000690	gene_with_dicistronic_transcript	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes an mRNA that is recoded." [SO:xp]	SO	399832	SO:0000693	SO:0001217	gene_with_recoded_mRNA	SO:0000704
2	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SOFA	substitution	SOFA	SOFA	sequence	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SO	399833	SO:0000694	SO:0001483	SNP	SO:1000002
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence used in experiment." [SO:ke]	SO	399834	SO:0000695	SO:0001409	reagent	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SO	399835	SO:0000696	SO:0000695	oligo	SO:0001409
2	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	SO	399836	SO:0000697	SO:0000693	gene_with_stop_codon_read_through	SO:0001217
2	"A gene that encodes an mRNA that is recoded." [SO:xp]	\N	gene_with_recoded_mRNA	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	399837	SO:0000698	SO:0000697	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0000693
3	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	732708	SO:0000698	SO:0000693	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0001217
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A comment about the sequence." [SO:ke]	SO	399839	SO:0000700	SO:0001410	remark	SO:0000001
2	"A comment about the sequence." [SO:ke]	SOFA	remark	SOFA	SOFA	sequence	"A region of sequence where the validity of the base calling is questionable." [SO:ke]	SO	399840	SO:0000701	SO:0000413	possible_base_call_error	SO:0000700
2	"A comment about the sequence." [SO:ke]	SOFA	remark	SOFA	SOFA	sequence	"A region of sequence where there may have been an error in the assembly." [SO:ke]	SO	399841	SO:0000702	SO:0000413	possible_assembly_error	SO:0000700
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A region of sequence implicated in an experimental result." [SO:ke]	SO	399842	SO:0000703	SO:0000700	experimental_result_region	SO:0001410
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	SO	399843	SO:0000704	SO:0001411	gene	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SO	399844	SO:0000705	SO:0000657	tandem_repeat	SO:0001411
2	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SOFA	splice_site	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	399845	SO:0000706	SO:0001420	trans_splice_acceptor_site	SO:0000162
2	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	399846	SO:0000707	SO:0001420	trans_splice_donor_site	SO:0000162
2	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	399847	SO:0000708	SO:0000706	SL1_acceptor_site	SO:0001420
2	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	399848	SO:0000709	SO:0000706	SL2_acceptor_site	SO:0001420
2	"A gene that encodes an mRNA that is recoded." [SO:xp]	\N	gene_with_recoded_mRNA	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	SO	399849	SO:0000710	SO:0000697	gene_with_stop_codon_redefined_as_selenocysteine	SO:0000693
2	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene with mRNA recoded by translational bypass." [SO:xp]	SO	399850	SO:0000711	SO:0000693	gene_with_mRNA_recoded_by_translational_bypass	SO:0001217
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene with mRNA recoded by translational bypass." [SO:xp]	SO	732721	SO:0000711	SO:0001217	gene_with_mRNA_recoded_by_translational_bypass	SO:0000704
2	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene encoding a transcript that has a translational frameshift." [SO:xp]	SO	399852	SO:0000712	SO:0000693	gene_with_transcript_with_translational_frameshift	SO:0001217
2	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A motif that is active in the DNA form of the sequence." [SO:ke]	SO	399853	SO:0000713	SO:0000714	DNA_motif	SO:0001683
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	SO	399854	SO:0000714	SO:0001683	nucleotide_motif	SO:0001411
2	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	SOFA	sequence_motif	SOFA	SOFA	sequence	"A motif that is active in RNA sequence." [SO:ke]	SO	399855	SO:0000715	SO:0000714	RNA_motif	SO:0001683
2	"A transcript that is polycistronic." [SO:xp]	\N	polycistronic_transcript	\N	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	399856	SO:0000716	SO:0000079	dicistronic_mRNA	SO:0000078
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	399857	SO:0000716	SO:0000079	dicistronic_mRNA	SO:0000673
2	"A transcript that is polycistronic." [SO:xp]	\N	polycistronic_transcript	\N	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	399858	SO:0000716	SO:0000634	dicistronic_mRNA	SO:0000078
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	399859	SO:0000716	SO:0000634	dicistronic_mRNA	SO:0000234
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	732729	SO:0000716	SO:0000234	dicistronic_mRNA	SO:0000233
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	SO	399861	SO:0000717	SO:0001410	reading_frame	SO:0000001
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]	SO	399862	SO:0000718	SO:0000717	blocked_reading_frame	SO:0001410
2	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	\N	sequence	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SO	399863	SO:0000719	SO:0001876	ultracontig	SO:0000353
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposable element that is foreign." [SO:ke]	SO	399864	SO:0000720	SO:0000101	foreign_transposable_element	SO:0001039
2	"A gene that encodes a polycistronic transcript." [SO:xp]	\N	gene_with_polycistronic_transcript	\N	\N	sequence	"A gene that encodes a dicistronic primary transcript." [SO:xp]	SO	399865	SO:0000721	SO:0000692	gene_with_dicistronic_primary_transcript	SO:0000690
2	"A gene that encodes a polycistronic transcript." [SO:xp]	\N	gene_with_polycistronic_transcript	\N	\N	sequence	"A gene that encodes a polycistronic mRNA." [SO:xp]	SO	399866	SO:0000722	SO:0000692	gene_with_dicistronic_mRNA	SO:0000690
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]	SO	399867	SO:0000723	SO:0000298	iDNA	SO:0001411
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399868	SO:0000724	SO:0000296	oriT	SO:0001235
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399869	SO:0000724	SO:0000296	oriT	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	399870	SO:0000725	SO:0001527	transit_peptide	SO:0000839
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The simplest repeated component of a repeat region. A single repeat." [SO:ke]	SO	399871	SO:0000726	SO:0001411	repeat_unit	SO:0000001
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SO	399872	SO:0000727	SO:0001055	CRM	SO:0001679
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	399873	SO:0000728	SO:0100011	intein	SO:0000839
2	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	\N	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	399874	SO:0000728	SO:0100011	intein	SO:0001063
2	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]	SO	399875	SO:0000729	SO:0000010	intein_containing	SO:0000401
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SO	399876	SO:0000730	SO:0000143	gap	SO:0001410
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SO	399877	SO:0000730	SO:0000353	gap	SO:0001248
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature that is incomplete." [SO:ke]	SO	399878	SO:0000731	SO:0000905	fragmentary	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an unverified region." [SO:ke]	SO	399879	SO:0000732	SO:0000905	predicted	SO:0000733
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	399880	SO:0000734	SO:0000234	exemplar_mRNA	SO:0000233
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	399881	SO:0000736	SO:0000735	organelle_sequence	SO:0000400
2	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	399882	SO:0000737	SO:0000736	mitochondrial_sequence	SO:0000735
2	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	399883	SO:0000738	SO:0000736	nuclear_sequence	SO:0000735
2	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	399884	SO:0000739	SO:0000736	nucleomorphic_sequence	SO:0000735
2	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	399885	SO:0000740	SO:0000736	plastid_sequence	SO:0000735
2	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055]	SO	399886	SO:0000741	SO:0001026	kinetoplast	SO:0001260
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]	SO	399887	SO:0000742	SO:0001235	maxicircle	SO:0001411
2	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	399888	SO:0000743	SO:0000740	apicoplast_sequence	SO:0000736
2	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	399889	SO:0000744	SO:0000740	chromoplast_sequence	SO:0000736
2	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	399890	SO:0000745	SO:0000740	chloroplast_sequence	SO:0000736
2	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	399891	SO:0000746	SO:0000740	cyanelle_sequence	SO:0000736
2	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	399892	SO:0000747	SO:0000740	leucoplast_sequence	SO:0000736
2	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	399893	SO:0000748	SO:0000740	proplastid_sequence	SO:0000736
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	399894	SO:0000749	SO:0000735	plasmid_location	SO:0000400
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]	SO	399895	SO:0000750	SO:0000296	amplification_origin	SO:0001235
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]	SO	399896	SO:0000750	SO:0000296	amplification_origin	SO:0001411
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	399897	SO:0000751	SO:0000735	proviral_location	SO:0000400
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"" []	SO	399898	SO:0000752	SO:0001679	gene_group_regulatory_region	SO:0005836
3	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SO	732768	SO:0000753	SO:0000695	clone_insert	SO:0001409
2	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SO	399900	SO:0000753	SO:0000151	clone_insert	SO:0000695
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	399901	SO:0000754	SO:0000440	lambda_vector	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	399902	SO:0000754	SO:0000440	lambda_vector	SO:0001235
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"" []	SO	399903	SO:0000755	SO:0000440	plasmid_vector	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"" []	SO	399904	SO:0000755	SO:0000440	plasmid_vector	SO:0001235
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	732772	SO:0000755	SO:0001235	plasmid_vector	SO:0001411
2	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]	SO	399906	SO:0000756	SO:0000352	cDNA	SO:0000348
2	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	\N	DNA	\N	\N	sequence	"" []	SO	399907	SO:0000757	SO:0000756	single_stranded_cDNA	SO:0000352
2	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	\N	DNA	\N	\N	sequence	"" []	SO	399908	SO:0000758	SO:0000756	double_stranded_cDNA	SO:0000352
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	399909	SO:0000766	SO:0000253	pyrrolysyl_tRNA	SO:0000655
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A plasmid that may integrate with a chromosome." [SO:ma]	SO	399910	SO:0000768	SO:0000155	episome	SO:0001235
2	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	\N	tmRNA	\N	\N	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	399911	SO:0000769	SO:0000847	tmRNA_coding_piece	SO:0000584
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	399912	SO:0000769	SO:0000847	tmRNA_coding_piece	SO:0000834
2	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	\N	tmRNA	\N	\N	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	399913	SO:0000770	SO:0000847	tmRNA_acceptor_piece	SO:0000584
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	399914	SO:0000770	SO:0000847	tmRNA_acceptor_piece	SO:0000834
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]	SO	399915	SO:0000771	SO:0001411	QTL	SO:0000001
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	SO	399916	SO:0000772	SO:0001039	genomic_island	SO:0001037
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	SO	399917	SO:0000773	SO:0000772	pathogenic_island	SO:0001039
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	399918	SO:0000774	SO:0000772	metabolic_island	SO:0001039
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	SO	399919	SO:0000775	SO:0000772	adaptive_island	SO:0001039
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	399920	SO:0000776	SO:0000772	symbiosis_island	SO:0001039
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A non functional descendant of an rRNA." [SO:ke]	SO	399921	SO:0000777	SO:0000462	pseudogenic_rRNA	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A non functional descendent of a tRNA." [SO:ke]	SO	399922	SO:0000778	SO:0000462	pseudogenic_tRNA	SO:0001411
2	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"An episome that is engineered." [SO:xp]	SO	399923	SO:0000779	SO:0000637	engineered_episome	SO:0000155
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"An episome that is engineered." [SO:xp]	SO	399924	SO:0000779	SO:0000637	engineered_episome	SO:0000804
2	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"An episome that is engineered." [SO:xp]	SO	399925	SO:0000779	SO:0000768	engineered_episome	SO:0000155
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Attribute describing sequence that has been integrated with foreign sequence." [SO:ke]	SO	399926	SO:0000781	SO:0000733	transgenic	SO:0000400
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a feature that occurs in nature." [SO:ke]	SO	399927	SO:0000782	SO:0000733	natural	SO:0000400
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a region that was modified in vitro." [SO:ke]	SO	399928	SO:0000783	SO:0000733	engineered	SO:0000400
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a region from another species." [SO:ke]	SO	399929	SO:0000784	SO:0000733	foreign	SO:0000400
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"" []	SO	1165691	SO:0000785	SO:0000695	cloned_region	SO:0001409
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	SOFA	sequence	"" []	SO	399931	SO:0000785	SO:0000753	cloned_region	SO:0000151
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"" []	SO	399932	SO:0000785	SO:0000753	cloned_region	SO:0000695
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature that has been proven." [SO:ke]	SO	399933	SO:0000789	SO:0000905	validated	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a feature that is invalidated." [SO:ke]	SO	399934	SO:0000790	SO:0000905	invalidated	SO:0000733
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	\N	sequence	"A rescue region that is engineered." [SO:xp]	SO	399935	SO:0000794	SO:0000411	engineered_rescue_region	SO:0000695
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A rescue region that is engineered." [SO:xp]	SO	399936	SO:0000794	SO:0000804	engineered_rescue_region	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A rescue region that is engineered." [SO:xp]	SO	399937	SO:0000794	SO:0000804	engineered_rescue_region	SO:0001409
2	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	\N	ORF	SOFA	\N	sequence	"A mini_gene that rescues." [SO:xp]	SO	399938	SO:0000795	SO:0000815	rescue_mini_gene	SO:0000236
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	SO	399939	SO:0000796	SO:0000101	transgenic_transposable_element	SO:0001039
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	399940	SO:0000797	SO:0000101	natural_transposable_element	SO:0001039
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	399941	SO:0000797	SO:0001038	natural_transposable_element	SO:0001037
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	399942	SO:0000798	SO:0000101	engineered_transposable_element	SO:0001039
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	399943	SO:0000798	SO:0000804	engineered_transposable_element	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	399944	SO:0000798	SO:0000804	engineered_transposable_element	SO:0001409
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	399945	SO:0000799	SO:0000720	engineered_foreign_transposable_element	SO:0000101
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	399946	SO:0000799	SO:0000798	engineered_foreign_transposable_element	SO:0000101
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	399947	SO:0000799	SO:0000798	engineered_foreign_transposable_element	SO:0000804
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	399948	SO:0000799	SO:0000805	engineered_foreign_transposable_element	SO:0000001
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	399949	SO:0000799	SO:0000805	engineered_foreign_transposable_element	SO:0000804
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	732811	SO:0000799	SO:0000101	engineered_foreign_transposable_element	SO:0001039
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	399951	SO:0000800	SO:0001504	assortment_derived_duplication	SO:0000240
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	399952	SO:0000801	SO:0001504	assortment_derived_deficiency_plus_duplication	SO:0000240
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	399953	SO:0000802	SO:0001504	assortment_derived_deficiency	SO:0000240
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	399954	SO:0000803	SO:0001504	assortment_derived_aneuploid	SO:0000240
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region that is engineered." [SO:xp]	SO	399955	SO:0000804	SO:0001409	engineered_region	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region that is engineered." [SO:xp]	SO	732824	SO:0000804	SO:0000001	engineered_region	SO:0000110
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A region that is engineered and foreign." [SO:xp]	SO	399957	SO:0000805	SO:0000804	engineered_foreign_region	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A region that is engineered and foreign." [SO:xp]	SO	399958	SO:0000805	SO:0000804	engineered_foreign_region	SO:0001409
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region that is engineered and foreign." [SO:xp]	SO	1165716	SO:0000805	SO:0000001	engineered_foreign_region	SO:0000110
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	399960	SO:0000806	SO:0000733	fusion	SO:0000400
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A tag that is engineered." [SO:xp]	SO	399961	SO:0000807	SO:0000324	engineered_tag	SO:0000696
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A tag that is engineered." [SO:xp]	SO	399962	SO:0000807	SO:0000804	engineered_tag	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A tag that is engineered." [SO:xp]	SO	399963	SO:0000807	SO:0000804	engineered_tag	SO:0001409
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A cDNA clone that has been validated." [SO:xp]	SO	399964	SO:0000808	SO:0000317	validated_cDNA_clone	SO:0000151
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A cDNA clone that is invalid." [SO:xp]	SO	399965	SO:0000809	SO:0000317	invalidated_cDNA_clone	SO:0000151
2	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	\N	cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated because it is chimeric." [SO:xp]	SO	399966	SO:0000810	SO:0000809	chimeric_cDNA_clone	SO:0000317
2	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	\N	cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated by genomic contamination." [SO:xp]	SO	399967	SO:0000811	SO:0000809	genomically_contaminated_cDNA_clone	SO:0000317
2	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	\N	cDNA_clone	\N	\N	sequence	"A cDNA clone invalidated by polyA priming." [SO:xp]	SO	399968	SO:0000812	SO:0000809	polyA_primed_cDNA_clone	SO:0000317
2	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	\N	cDNA_clone	\N	\N	sequence	"A cDNA invalidated clone by partial processing." [SO:xp]	SO	399969	SO:0000813	SO:0000809	partially_processed_cDNA_clone	SO:0000317
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]	SO	399970	SO:0000814	SO:0000733	rescue	SO:0000400
2	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	\N	reading_frame	SOFA	SOFA	sequence	"By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]	SO	399971	SO:0000815	SO:0000236	mini_gene	SO:0000717
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that rescues." [SO:xp]	SO	399972	SO:0000816	SO:0000704	rescue_gene	SO:0001411
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]	SO	399973	SO:0000817	SO:0000733	wild_type	SO:0000400
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that rescues." [SO:xp]	SO	399974	SO:0000818	SO:0000816	wild_type_rescue_gene	SO:0000704
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that rescues." [SO:xp]	SO	732838	SO:0000818	SO:0000704	wild_type_rescue_gene	SO:0001411
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in a mitochondria." [SO:xp]	SO	399976	SO:0000819	SO:0000340	mitochondrial_chromosome	SO:0001235
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in a chloroplast." [SO:xp]	SO	399977	SO:0000820	SO:0000340	chloroplast_chromosome	SO:0001235
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in a chromoplast." [SO:xp]	SO	399978	SO:0000821	SO:0000340	chromoplast_chromosome	SO:0001235
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in a cyanelle." [SO:xp]	SO	399979	SO:0000822	SO:0000340	cyanelle_chromosome	SO:0001235
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome with origin in a leucoplast." [SO:xp]	SO	399980	SO:0000823	SO:0000340	leucoplast_chromosome	SO:0001235
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in a macronucleus." [SO:xp]	SO	399981	SO:0000824	SO:0000340	macronuclear_chromosome	SO:0001235
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in a micronucleus." [SO:xp]	SO	399982	SO:0000825	SO:0000340	micronuclear_chromosome	SO:0001235
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in a nucleus." [SO:xp]	SO	399983	SO:0000828	SO:0000340	nuclear_chromosome	SO:0001235
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in a nucleomorph." [SO:xp]	SO	399984	SO:0000829	SO:0000340	nucleomorphic_chromosome	SO:0001235
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of a chromosome." [SO:ke]	SO	1165737	SO:0000830	SO:0001411	chromosome_part	SO:0000001
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"A region of a chromosome." [SO:ke]	SO	399986	SO:0000830	SO:0000340	chromosome_part	SO:0001235
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of a gene." [SO:ke]	SO	399987	SO:0000831	SO:0001411	gene_member_region	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of a transcript." [SO:ke]	SO	1165738	SO:0000833	SO:0001411	transcript_region	SO:0000001
2	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of a transcript." [SO:ke]	SO	399989	SO:0000833	SO:0000673	transcript_region	SO:0000831
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of a mature transcript." [SO:ke]	SO	399990	SO:0000834	SO:0000833	mature_transcript_region	SO:0000673
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a mature transcript." [SO:ke]	SO	399991	SO:0000834	SO:0000833	mature_transcript_region	SO:0001411
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	399992	SO:0000835	SO:0000833	primary_transcript_region	SO:0000673
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	399993	SO:0000835	SO:0000833	primary_transcript_region	SO:0001411
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	399994	SO:0000835	SO:0000185	primary_transcript_region	SO:0000673
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	399995	SO:0000836	SO:0000834	mRNA_region	SO:0000833
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	399996	SO:0000836	SO:0000234	mRNA_region	SO:0000233
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	399997	SO:0000837	SO:0000836	UTR_region	SO:0000234
2	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	399998	SO:0000837	SO:0000836	UTR_region	SO:0000834
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	399999	SO:0000838	SO:0000835	rRNA_primary_transcript_region	SO:0000185
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	400000	SO:0000838	SO:0000835	rRNA_primary_transcript_region	SO:0000833
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	400001	SO:0000838	SO:0000209	rRNA_primary_transcript_region	SO:0000483
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens,SOFA	region	SOFA	SOFA	sequence	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	SO	732868	SO:0000839	SO:0001411	polypeptide_region	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	SOFA	sequence	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	SO	400003	SO:0000839	SO:0000104	polypeptide_region	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a repeated sequence." [SO:ke]	SO	400004	SO:0000840	SO:0001412	repeat_component	SO:0000001
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	1165753	SO:0000841	SO:0000835	spliceosomal_intron_region	SO:0000185
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	1165754	SO:0000841	SO:0000835	spliceosomal_intron_region	SO:0000833
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	intron	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	400007	SO:0000841	SO:0000662	spliceosomal_intron_region	SO:0000188
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"" []	SO	732875	SO:0000842	SO:0001411	gene_component_region	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"" []	SO	400009	SO:0000842	SO:0000704	gene_component_region	SO:0001411
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	400010	SO:0000847	SO:0000834	tmRNA_region	SO:0000833
2	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"A region of a tmRNA." [SO:cb]	SO	400011	SO:0000847	SO:0000584	tmRNA_region	SO:0000370
2	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	400012	SO:0000848	SO:0000840	LTR_component	SO:0001412
2	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	400013	SO:0000848	SO:0000286	LTR_component	SO:0000186
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	400014	SO:0000848	SO:0000286	LTR_component	SO:0000657
2	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	400015	SO:0000849	SO:0000848	three_prime_LTR_component	SO:0000286
2	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	400016	SO:0000849	SO:0000848	three_prime_LTR_component	SO:0000840
2	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	400017	SO:0000849	SO:0000426	three_prime_LTR_component	SO:0000286
2	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	400018	SO:0000850	SO:0000848	five_prime_LTR_component	SO:0000286
2	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	400019	SO:0000850	SO:0000848	five_prime_LTR_component	SO:0000840
2	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	400020	SO:0000850	SO:0000425	five_prime_LTR_component	SO:0000286
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	732890	SO:0000851	SO:0000836	CDS_region	SO:0000234
3	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	732891	SO:0000851	SO:0000836	CDS_region	SO:0000834
2	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	400023	SO:0000851	SO:0000316	CDS_region	SO:0000836
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	732894	SO:0000852	SO:0000833	exon_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	732895	SO:0000852	SO:0000833	exon_region	SO:0001411
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	400026	SO:0000852	SO:0000147	exon_region	SO:0000833
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region that is homologous to another region." [SO:ke]	SO	400027	SO:0000853	SO:0000330	homologous_region	SO:0001410
2	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A homologous_region that is paralogous to another region." [SO:ke]	SO	400028	SO:0000854	SO:0000853	paralogous_region	SO:0000330
2	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"A homologous_region that is orthologous to another region." [SO:ke]	SO	400029	SO:0000855	SO:0000853	orthologous_region	SO:0000330
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	400030	SO:0000856	SO:0000733	conserved	SO:0000400
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Similarity due to common ancestry." [SO:ke]	SO	400031	SO:0000857	SO:0000856	homologous	SO:0000733
2	"" []	\N	conserved	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]	SO	400032	SO:0000858	SO:0000857	orthologous	SO:0000856
2	"" []	\N	conserved	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]	SO	400033	SO:0000859	SO:0000857	paralogous	SO:0000856
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]	SO	400034	SO:0000860	SO:0000856	syntenic	SO:0000733
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript that is capped." [SO:xp]	SO	400035	SO:0000861	SO:0000185	capped_primary_transcript	SO:0000673
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA that is capped." [SO:xp]	SO	400036	SO:0000862	SO:0000234	capped_mRNA	SO:0000233
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an mRNA feature." [SO:ke]	SO	400037	SO:0000863	SO:0000237	mRNA_attribute	SO:0000733
2	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]	SO	400038	SO:0000864	SO:0000863	exemplar	SO:0000237
2	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	SO	400039	SO:0000865	SO:0000863	frameshift	SO:0000237
2	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"A frameshift caused by deleting one base." [SO:ke]	SO	400040	SO:0000866	SO:0000865	minus_1_frameshift	SO:0000863
2	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"A frameshift caused by deleting two bases." [SO:ke]	SO	400041	SO:0000867	SO:0000865	minus_2_frameshift	SO:0000863
2	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"A frameshift caused by inserting one base." [SO:ke]	SO	400042	SO:0000868	SO:0000865	plus_1_frameshift	SO:0000863
2	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"A frameshift caused by inserting two bases." [SO:ke]	SO	400043	SO:0000869	SO:0000865	plus_2_framshift	SO:0000863
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]	SO	400044	SO:0000870	SO:0000237	trans_spliced	SO:0000733
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA that is polyadenylated." [SO:xp]	SO	400045	SO:0000871	SO:0000234	polyadenylated_mRNA	SO:0000233
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	400046	SO:0000872	SO:0000234	trans_spliced_mRNA	SO:0000233
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	400047	SO:0000872	SO:0000479	trans_spliced_mRNA	SO:0000673
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is edited." [SO:ke]	SO	400048	SO:0000873	SO:0000673	edited_transcript	SO:0000831
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A transcript that has been edited by A to I substitution." [SO:ke]	SO	400049	SO:0000874	SO:0000873	edited_transcript_by_A_to_I_substitution	SO:0000673
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that is bound by a protein." [SO:ke]	SO	400050	SO:0000875	SO:0000277	bound_by_protein	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]	SO	400051	SO:0000876	SO:0000277	bound_by_nucleic_acid	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]	SO	400052	SO:0000877	SO:0000237	alternatively_spliced	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for one gene product." [SO:ke]	SO	400053	SO:0000878	SO:0000237	monocistronic	SO:0000733
2	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for two gene products." [SO:ke]	SO	400054	SO:0000879	SO:0000880	dicistronic	SO:0000237
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]	SO	400055	SO:0000880	SO:0000237	polycistronic	SO:0000733
2	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	SO	400056	SO:0000881	SO:0000863	recoded	SO:0000237
2	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"An attribute describing the alteration of codon meaning." [SO:ke]	SO	400057	SO:0000882	SO:0000881	codon_redefined	SO:0000863
2	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	\N	codon	SOFA	\N	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	400058	SO:0000883	SO:0000145	stop_codon_read_through	SO:0000360
2	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	\N	recoded_codon	\N	\N	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	400059	SO:0000884	SO:0000883	stop_codon_redefined_as_pyrrolysine	SO:0000145
2	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	\N	recoded_codon	\N	\N	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	400060	SO:0000885	SO:0000883	stop_codon_redefined_as_selenocysteine	SO:0000145
2	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"Recoded mRNA where a block of nucleotides is not translated." [SO:ke]	SO	400061	SO:0000886	SO:0000881	recoded_by_translational_bypass	SO:0000863
2	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"Recoding by frameshifting a particular site." [SO:ke]	SO	400062	SO:0000887	SO:0000881	translationally_frameshifted	SO:0000863
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	400063	SO:0000888	SO:0000898	maternally_imprinted_gene	SO:0000704
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	400064	SO:0000888	SO:0000898	maternally_imprinted_gene	SO:0001720
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	732931	SO:0000888	SO:0000704	maternally_imprinted_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	400066	SO:0000889	SO:0000898	paternally_imprinted_gene	SO:0000704
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	400067	SO:0000889	SO:0000898	paternally_imprinted_gene	SO:0001720
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	732934	SO:0000889	SO:0000704	paternally_imprinted_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is post translationally regulated." [SO:xp]	SO	400069	SO:0000890	SO:0000704	post_translationally_regulated_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is negatively autoreguated." [SO:xp]	SO	400070	SO:0000891	SO:0000704	negatively_autoregulated_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is positively autoregulated." [SO:xp]	SO	400071	SO:0000892	SO:0000704	positively_autoregulated_gene	SO:0001411
2	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	SO	400072	SO:0000893	SO:0000126	silenced	SO:0000123
2	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	SO	400073	SO:0000894	SO:0000893	silenced_by_DNA_modification	SO:0000126
2	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	\N	silenced	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	400074	SO:0000895	SO:0000894	silenced_by_DNA_methylation	SO:0000893
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is translationally regulated." [SO:xp]	SO	400075	SO:0000896	SO:0000704	translationally_regulated_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is allelically_excluded." [SO:xp]	SO	400076	SO:0000897	SO:0000898	allelically_excluded_gene	SO:0000704
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A gene that is allelically_excluded." [SO:xp]	SO	400077	SO:0000897	SO:0000898	allelically_excluded_gene	SO:0001720
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is epigenetically modified." [SO:ke]	SO	400078	SO:0000898	SO:0000704	epigenetically_modified_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is epigenetically modified." [SO:ke]	SO	400079	SO:0000898	SO:0001720	epigenetically_modified_gene	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]	SO	400080	SO:0000902	SO:0000704	transgene	SO:0001411
2	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	400081	SO:0000903	SO:0000751	endogenous_retroviral_sequence	SO:0000735
2	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]	SO	400082	SO:0000904	SO:0000133	rearranged_at_DNA_level	SO:0000401
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	SO	400083	SO:0000905	SO:0000733	status	SO:0000400
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Attribute to describe a feature that is independently known - not predicted." [SO:ke]	SO	400084	SO:0000906	SO:0000905	independently_known	SO:0000733
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]	SO	400085	SO:0000907	SO:0000732	supported_by_sequence_similarity	SO:0000905
2	"An attribute describing an unverified region." [SO:ke]	\N	predicted	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]	SO	400086	SO:0000908	SO:0000907	supported_by_domain_match	SO:0000732
2	"An attribute describing an unverified region." [SO:ke]	\N	predicted	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]	SO	400087	SO:0000909	SO:0000907	supported_by_EST_or_cDNA	SO:0000732
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"" []	SO	400088	SO:0000910	SO:0000732	orphan	SO:0000905
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]	SO	400089	SO:0000911	SO:0000732	predicted_by_ab_initio_computation	SO:0000905
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400090	SO:0000912	SO:0001128	asx_turn	SO:0001078
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	SOFA	sequence	"A clone insert made from cDNA." [SO:xp]	SO	400091	SO:0000913	SO:0000753	cloned_cDNA_insert	SO:0000151
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A clone insert made from cDNA." [SO:xp]	SO	400092	SO:0000913	SO:0000753	cloned_cDNA_insert	SO:0000695
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	SOFA	sequence	"A clone insert made from genomic DNA." [SO:xp]	SO	400093	SO:0000914	SO:0000753	cloned_genomic_insert	SO:0000151
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A clone insert made from genomic DNA." [SO:xp]	SO	400094	SO:0000914	SO:0000753	cloned_genomic_insert	SO:0000695
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	SOFA	sequence	"A clone insert that is engineered." [SO:xp]	SO	400095	SO:0000915	SO:0000753	engineered_insert	SO:0000151
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A clone insert that is engineered." [SO:xp]	SO	400096	SO:0000915	SO:0000753	engineered_insert	SO:0000695
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A clone insert that is engineered." [SO:xp]	SO	400097	SO:0000915	SO:0000804	engineered_insert	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A clone insert that is engineered." [SO:xp]	SO	400098	SO:0000915	SO:0000804	engineered_insert	SO:0001409
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA that is edited." [SO:xp]	SO	400099	SO:0000929	SO:0000234	edited_mRNA	SO:0000233
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"An mRNA that is edited." [SO:xp]	SO	400100	SO:0000929	SO:0000873	edited_mRNA	SO:0000673
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	400101	SO:0000930	SO:0000834	guide_RNA_region	SO:0000833
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	400102	SO:0000930	SO:0000602	guide_RNA_region	SO:0000655
2	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	\N	guide_RNA	SOFA	\N	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	400103	SO:0000931	SO:0000930	anchor_region	SO:0000602
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	400104	SO:0000931	SO:0000930	anchor_region	SO:0000834
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	400105	SO:0000932	SO:0000120	pre_edited_mRNA	SO:0000185
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature between stages of processing." [SO:ke]	SO	400106	SO:0000933	SO:0000733	intermediate	SO:0000400
2	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	\N	sequence	"A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]	SO	400107	SO:0000934	SO:0001655	miRNA_target_site	SO:0000409
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	400108	SO:0000935	SO:0000316	edited_CDS	SO:0000836
2	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	400109	SO:0000936	SO:0000301	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000300
2	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	400110	SO:0000938	SO:0000301	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000300
2	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	400111	SO:0000939	SO:0000301	vertebrate_immune_system_gene_recombination_signal_feature	SO:0000300
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	400112	SO:0000940	SO:0000733	recombinationally_rearranged	SO:0000400
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]	SO	400113	SO:0000941	SO:0000456	recombinationally_rearranged_vertebrate_immune_system_gene	SO:0000704
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	400114	SO:0000942	SO:0000946	attP_site	SO:0000342
2	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	400115	SO:0000942	SO:0001042	attP_site	SO:0001041
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	400116	SO:0000943	SO:0000946	attB_site	SO:0000342
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	400117	SO:0000944	SO:0000946	attL_site	SO:0000342
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	400118	SO:0000945	SO:0000946	attR_site	SO:0000342
2	"" []	\N	specific_recombination_site	\N	\N	sequence	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	SO	400119	SO:0000946	SO:0000342	integration_excision_site	SO:0000299
2	"" []	\N	specific_recombination_site	\N	\N	sequence	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	SO	400120	SO:0000947	SO:0000342	resolution_site	SO:0000299
2	"" []	\N	specific_recombination_site	\N	\N	sequence	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	SO	400121	SO:0000948	SO:0000342	inversion_site	SO:0000299
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	400122	SO:0000949	SO:0000947	dif_site	SO:0000342
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	400123	SO:0000950	SO:0000946	attC_site	SO:0000342
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	400124	SO:0000950	SO:0000365	attC_site	SO:0001039
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	400125	SO:0000951	SO:0000141	eukaryotic_terminator	SO:0000673
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	400126	SO:0000951	SO:0000141	eukaryotic_terminator	SO:0001679
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"An origin of vegetative replication in plasmids and phages." [SO:as]	SO	400127	SO:0000952	SO:0000296	oriV	SO:0001235
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An origin of vegetative replication in plasmids and phages." [SO:as]	SO	400128	SO:0000952	SO:0000296	oriV	SO:0001411
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"An origin of bacterial chromosome replication." [SO:as]	SO	400129	SO:0000953	SO:0000296	oriC	SO:0001235
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An origin of bacterial chromosome replication." [SO:as]	SO	400130	SO:0000953	SO:0000296	oriC	SO:0001411
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	SO	400131	SO:0000954	SO:0000340	DNA_chromosome	SO:0001235
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	SO	400132	SO:0000955	SO:0000954	double_stranded_DNA_chromosome	SO:0000340
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	SO	400133	SO:0000956	SO:0000954	single_stranded_DNA_chromosome	SO:0000340
2	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	\N	DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	SO	400134	SO:0000957	SO:0000955	linear_double_stranded_DNA_chromosome	SO:0000954
2	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	\N	DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	SO	400135	SO:0000958	SO:0000955	circular_double_stranded_DNA_chromosome	SO:0000954
2	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	\N	DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	SO	400136	SO:0000959	SO:0000956	linear_single_stranded_DNA_chromosome	SO:0000954
2	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	\N	DNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	400137	SO:0000960	SO:0000956	circular_single_stranded_DNA_chromosome	SO:0000954
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	SO	400138	SO:0000961	SO:0000340	RNA_chromosome	SO:0001235
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	SO	400139	SO:0000962	SO:0000961	single_stranded_RNA_chromosome	SO:0000340
2	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	\N	RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	SO	400140	SO:0000963	SO:0000962	linear_single_stranded_RNA_chromosome	SO:0000961
2	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	\N	RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	SO	400141	SO:0000964	SO:0000965	linear_double_stranded_RNA_chromosome	SO:0000961
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	SO	400142	SO:0000965	SO:0000961	double_stranded_RNA_chromosome	SO:0000340
2	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	\N	RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	400143	SO:0000966	SO:0000962	circular_single_stranded_RNA_chromosome	SO:0000961
2	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	\N	RNA_chromosome	\N	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	SO	400144	SO:0000967	SO:0000965	circular_double_stranded_RNA_chromosome	SO:0000961
2	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	400145	SO:0000973	SO:0000208	insertion_sequence	SO:0000182
2	"A gene located in mitochondrial sequence." [SO:xp]	\N	mt_gene	\N	\N	sequence	"" []	SO	400146	SO:0000975	SO:0000089	minicircle_gene	SO:0000088
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"" []	SO	400147	SO:0000975	SO:0000980	minicircle_gene	SO:0001235
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke]	SO	400148	SO:0000976	SO:0000733	cryptic	SO:0000400
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	400149	SO:0000977	SO:0000833	anchor_binding_site	SO:0000673
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	400150	SO:0000977	SO:0000833	anchor_binding_site	SO:0001411
2	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	\N	guide_RNA	SOFA	\N	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	400151	SO:0000978	SO:0000930	template_region	SO:0000602
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	400152	SO:0000978	SO:0000930	template_region	SO:0000834
2	"" []	\N	gene_attribute	\N	\N	sequence	"A non-protein_coding gene that encodes a guide_RNA." [SO:ma]	SO	400153	SO:0000979	SO:0000011	gRNA_encoding	SO:0000401
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]	SO	400154	SO:0000980	SO:0001235	minicircle	SO:0001411
2	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	terminator	SOFA	\N	sequence	"" []	SO	400155	SO:0000981	SO:0000614	rho_dependent_bacterial_terminator	SO:0000141
2	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"" []	SO	400156	SO:0000981	SO:0000614	rho_dependent_bacterial_terminator	SO:0000752
2	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	terminator	SOFA	\N	sequence	"" []	SO	400157	SO:0000982	SO:0000614	rho_independent_bacterial_terminator	SO:0000141
2	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"" []	SO	400158	SO:0000982	SO:0000614	rho_independent_bacterial_terminator	SO:0000752
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	400159	SO:0000983	SO:0000733	strand_attribute	SO:0000400
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400160	SO:0000984	SO:0000983	single	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400161	SO:0000985	SO:0000983	double	SO:0000733
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	400162	SO:0000986	SO:0000443	topology_attribute	SO:0000400
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]	SO	400163	SO:0000987	SO:0000986	linear	SO:0000443
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]	SO	400164	SO:0000988	SO:0000986	circular	SO:0000443
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	400165	SO:0000989	SO:0000655	class_II_RNA	SO:0000233
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	400166	SO:0000990	SO:0000655	class_I_RNA	SO:0000233
2	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"" []	SO	400167	SO:0000991	SO:0000352	genomic_DNA	SO:0000348
2	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	\N	clone_insert	SOFA	\N	sequence	"" []	SO	400168	SO:0000992	SO:0000914	BAC_cloned_genomic_insert	SO:0000753
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400169	SO:0000993	SO:0000905	consensus	SO:0000733
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	400170	SO:0000994	SO:0001410	consensus_region	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	733037	SO:0000994	SO:0000001	consensus_region	SO:0000110
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"" []	SO	400172	SO:0000995	SO:0000234	consensus_mRNA	SO:0000233
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"" []	SO	400173	SO:0000995	SO:0000994	consensus_mRNA	SO:0000001
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"" []	SO	400174	SO:0000995	SO:0000994	consensus_mRNA	SO:0001410
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	400175	SO:0000996	SO:0000704	predicted_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	SOFA	sequence	"" []	SO	400176	SO:0000997	SO:0000842	gene_fragment	SO:0000704
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	400177	SO:0000997	SO:0000842	gene_fragment	SO:0001411
2	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	400178	SO:0000998	SO:0001419	recursive_splice_site	SO:0000162
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	400179	SO:0000999	SO:0000150	BAC_end	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	400180	SO:0000999	SO:0000150	BAC_end	SO:0000149
2	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	400181	SO:0000999	SO:0000153	BAC_end	SO:0000440
2	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	400182	SO:0001000	SO:0000650	rRNA_16S	SO:0000252
2	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	400183	SO:0001001	SO:0000651	rRNA_23S	SO:0000252
2	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SOFA	rRNA	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	400184	SO:0001002	SO:0000651	rRNA_25S	SO:0000252
2	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	400185	SO:0001003	SO:0000286	solo_LTR	SO:0000186
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	400186	SO:0001003	SO:0000286	solo_LTR	SO:0000657
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400187	SO:0001004	SO:0000905	low_complexity	SO:0000733
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	400188	SO:0001005	SO:0001410	low_complexity_region	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	733057	SO:0001005	SO:0000001	low_complexity_region	SO:0000110
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	SO	400190	SO:0001006	SO:0000113	prophage	SO:0001039
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	SO	400191	SO:0001007	SO:0000772	cryptic_prophage	SO:0001039
2	"A folded RNA sequence." [SO:ke]	\N	RNA_sequence_secondary_structure	\N	\N	sequence	"A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]	SO	400192	SO:0001008	SO:0000313	tetraloop	SO:0000122
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	SO	400193	SO:0001009	SO:0000442	DNA_constraint_sequence	SO:0000696
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]	SO	400194	SO:0001010	SO:0000142	i_motif	SO:0000002
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]	SO	400195	SO:0001011	SO:0001247	PNA_oligo	SO:0000696
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A DNA sequence with catalytic activity." [SO:cb]	SO	400196	SO:0001012	SO:0000696	DNAzyme	SO:0000695
2	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	\N	sequence	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	SO	400197	SO:0001013	SO:0002007	MNP	SO:1000002
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	733070	SO:0001014	SO:0000835	intron_domain	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	733071	SO:0001014	SO:0000835	intron_domain	SO:0000833
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"" []	SO	400200	SO:0001014	SO:0000188	intron_domain	SO:0000835
2	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]	SO	400201	SO:0001015	SO:0000028	wobble_base_pair	SO:0000002
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	400202	SO:0001016	SO:0001014	internal_guide_sequence	SO:0000188
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	400203	SO:0001016	SO:0001014	internal_guide_sequence	SO:0000835
2	"A self spliced intron." [SO:ke]	\N	autocatalytically_spliced_intron	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	400204	SO:0001016	SO:0000587	internal_guide_sequence	SO:0000588
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke]	SO	400205	SO:0001017	SO:0001878	silent_mutation	SO:0001537
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]	SO	400206	SO:0001018	SO:0000409	epitope	SO:0001411
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A variation that increases or decreases the copy number of a given region." [SO:ke]	SO	400207	SO:0001019	SO:0001059	copy_number_variation	SO:0000110
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	400208	SO:0001021	SO:0000699	chromosome_breakpoint	SO:0000110
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"" []	SO	400209	SO:0001021	SO:0000340	chromosome_breakpoint	SO:0001235
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	400210	SO:0001022	SO:0001021	inversion_breakpoint	SO:0000340
2	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	400211	SO:0001022	SO:0001021	inversion_breakpoint	SO:0000699
2	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]	SO	400212	SO:0001023	SO:0001507	allele	SO:0001260
2	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]	SO	400213	SO:0001024	SO:0001507	haplotype	SO:0001260
2	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]	SO	400214	SO:0001025	SO:0001023	polymorphic_sequence_variant	SO:0001507
2	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]	SO	400215	SO:0001027	SO:0001507	genotype	SO:0001260
2	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]	SO	400216	SO:0001028	SO:0001507	diplotype	SO:0001260
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	400217	SO:0001029	SO:0000733	direction_attribute	SO:0000400
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]	SO	400218	SO:0001030	SO:0001029	forward	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke]	SO	400219	SO:0001031	SO:0001029	reverse	SO:0000733
2	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	400220	SO:0001032	SO:0000737	mitochondrial_DNA	SO:0000736
2	"" []	\N	plastid_sequence	\N	\N	sequence	"" []	SO	400221	SO:0001033	SO:0000745	chloroplast_DNA	SO:0000740
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	400222	SO:0001034	SO:0001014	mirtron	SO:0000188
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	400223	SO:0001034	SO:0001014	mirtron	SO:0000835
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	SO	400224	SO:0001035	SO:0000655	piRNA	SO:0000233
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	400225	SO:0001036	SO:0000253	arginyl_tRNA	SO:0000655
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SO	400226	SO:0001037	SO:0001411	mobile_genetic_element	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	SO	733092	SO:0001037	SO:0000001	mobile_genetic_element	SO:0000110
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An MGE that is not integrated into the host chromosome." [SO:ke]	SO	400228	SO:0001038	SO:0001037	extrachromosomal_mobile_genetic_element	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An MGE that is not integrated into the host chromosome." [SO:ke]	SO	400229	SO:0001038	SO:0001037	extrachromosomal_mobile_genetic_element	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An MGE that is integrated into the host chromosome." [SO:ke]	SO	400230	SO:0001039	SO:0001037	integrated_mobile_genetic_element	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An MGE that is integrated into the host chromosome." [SO:ke]	SO	400231	SO:0001039	SO:0001037	integrated_mobile_genetic_element	SO:0001411
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A plasmid sequence that is integrated within the host chromosome." [SO:ke]	SO	400232	SO:0001040	SO:0001039	integrated_plasmid	SO:0001037
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	400233	SO:0001041	SO:0001038	viral_sequence	SO:0001037
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	400234	SO:0001041	SO:0001235	viral_sequence	SO:0001411
2	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	400235	SO:0001042	SO:0001041	phage_sequence	SO:0001038
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	400236	SO:0001042	SO:0001041	phage_sequence	SO:0001235
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	400237	SO:0001043	SO:0000946	attCtn_site	SO:0000342
2	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	400238	SO:0001043	SO:0000371	attCtn_site	SO:0000182
2	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]	SO	400239	SO:0001044	SO:0001760	nuclear_mt_pseudogene	SO:0000336
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]	SO	400240	SO:0001045	SO:0001039	cointegrated_plasmid	SO:0001037
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	400241	SO:0001046	SO:0001048	IRLinv_site	SO:0000342
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	400242	SO:0001046	SO:0000948	IRLinv_site	SO:0000342
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	400243	SO:0001047	SO:0001048	IRRinv_site	SO:0000342
2	"" []	\N	site_specific_recombination_target_region	\N	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	400244	SO:0001047	SO:0000948	IRRinv_site	SO:0000342
2	"" []	\N	specific_recombination_site	\N	\N	sequence	"A region located within an inversion site." [SO:ke]	SO	400245	SO:0001048	SO:0000342	inversion_site_part	SO:0000299
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	\N	sequence	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	SO	400246	SO:0001049	SO:0000772	defective_conjugative_transposon	SO:0001039
2	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	400247	SO:0001050	SO:0000840	repeat_fragment	SO:0001412
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	400248	SO:0001050	SO:0001649	repeat_fragment	SO:0000657
2	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	400249	SO:0001054	SO:0000840	transposon_fragment	SO:0001412
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	400250	SO:0001054	SO:0001648	transposon_fragment	SO:0000101
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SO	400251	SO:0001055	SO:0001679	transcriptional_cis_regulatory_region	SO:0005836
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A regulatory_region that modulates splicing." [SO:ke]	SO	400252	SO:0001056	SO:0001679	splicing_regulatory_region	SO:0005836
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	SO	400253	SO:0001058	SO:0001055	promoter_targeting_sequence	SO:0001679
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	733123	SO:0001061	SO:0100011	propeptide_cleavage_site	SO:0000839
3	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	733124	SO:0001061	SO:0100011	propeptide_cleavage_site	SO:0001063
2	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	400256	SO:0001061	SO:0001062	propeptide_cleavage_site	SO:0100011
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	400257	SO:0001062	SO:0100011	propeptide	SO:0000839
2	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	400258	SO:0001062	SO:0100011	propeptide	SO:0001063
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens,SOFA	polypeptide	SOFA	biosapiens,SOFA	sequence	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	SO	400259	SO:0001063	SO:0000839	immature_peptide_region	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	SO	400260	SO:0001063	SO:0000839	immature_peptide_region	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	400261	SO:0001064	SO:0000419	active_peptide	SO:0000839
2	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	400262	SO:0001064	SO:0000419	active_peptide	SO:0001063
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]	SO	400263	SO:0001066	SO:0000839	compositionally_biased_region_of_peptide	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]	SO	400264	SO:0001066	SO:0000839	compositionally_biased_region_of_peptide	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	SO	400265	SO:0001067	SO:0100021	polypeptide_motif	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	SO	400266	SO:0001068	SO:0100021	polypeptide_repeat	SO:0000839
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	SO	400267	SO:0001070	SO:0000839	polypeptide_structural_region	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	SO	400268	SO:0001070	SO:0000839	polypeptide_structural_region	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	SO	400269	SO:0001071	SO:0001070	membrane_structure	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	733145	SO:0001072	SO:0001070	extramembrane_polypeptide_region	SO:0000839
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	400271	SO:0001072	SO:0001071	extramembrane_polypeptide_region	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	400272	SO:0001073	SO:0001072	cytoplasmic_polypeptide_region	SO:0001070
2	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	biosapiens	membrane_structure	biosapiens	biosapiens	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	400273	SO:0001073	SO:0001072	cytoplasmic_polypeptide_region	SO:0001071
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	400274	SO:0001074	SO:0001072	non_cytoplasmic_polypeptide_region	SO:0001070
2	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	biosapiens	membrane_structure	biosapiens	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	400275	SO:0001074	SO:0001072	non_cytoplasmic_polypeptide_region	SO:0001071
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	733152	SO:0001075	SO:0001070	intramembrane_polypeptide_region	SO:0000839
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	400277	SO:0001075	SO:0001071	intramembrane_polypeptide_region	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	400278	SO:0001076	SO:0001075	membrane_peptide_loop	SO:0001070
2	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	biosapiens	membrane_structure	biosapiens	biosapiens	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	400279	SO:0001076	SO:0001075	membrane_peptide_loop	SO:0001071
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	400280	SO:0001077	SO:0001075	transmembrane_polypeptide_region	SO:0001070
2	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	biosapiens	membrane_structure	biosapiens	biosapiens	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	400281	SO:0001077	SO:0001075	transmembrane_polypeptide_region	SO:0001071
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	SO	400282	SO:0001078	SO:0001070	polypeptide_secondary_structure	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	SO	400283	SO:0001079	SO:0001070	polypeptide_structural_motif	SO:0000839
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	400284	SO:0001080	SO:0001079	coiled_coil	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	400285	SO:0001081	SO:0001079	helix_turn_helix	SO:0001070
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	biosapiens	experimental_feature	SOFA	SOFA	sequence	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	SO	400286	SO:0001082	SO:0000700	polypeptide_sequencing_information	SO:0001410
2	"A comment about the sequence." [SO:ke]	biosapiens	remark	SOFA	biosapiens	sequence	"Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]	SO	400287	SO:0001083	SO:0001082	non_adjacent_residues	SO:0000700
2	"A comment about the sequence." [SO:ke]	biosapiens	remark	SOFA	biosapiens	sequence	"The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]	SO	400288	SO:0001084	SO:0001082	non_terminal_residue	SO:0000700
2	"A comment about the sequence." [SO:ke]	biosapiens	remark	SOFA	biosapiens	sequence	"Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]	SO	400289	SO:0001085	SO:0001082	sequence_conflict	SO:0000700
2	"A comment about the sequence." [SO:ke]	biosapiens	remark	SOFA	biosapiens	sequence	"Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]	SO	400290	SO:0001086	SO:0001082	sequence_uncertainty	SO:0000700
2	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	400291	SO:0001089	SO:0100001	post_translationally_modified_region	SO:0001067
2	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	400292	SO:0001092	SO:0001656	polypeptide_metal_contact	SO:0000409
2	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	400293	SO:0001092	SO:0100002	polypeptide_metal_contact	SO:0100001
2	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	SOFA	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	400294	SO:0001093	SO:0000410	protein_protein_contact	SO:0000409
2	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	400295	SO:0001093	SO:0100002	protein_protein_contact	SO:0100001
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	400296	SO:0001094	SO:0001092	polypeptide_calcium_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	400297	SO:0001094	SO:0001092	polypeptide_calcium_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	400298	SO:0001095	SO:0001092	polypeptide_cobalt_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	400299	SO:0001095	SO:0001092	polypeptide_cobalt_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	400300	SO:0001096	SO:0001092	polypeptide_copper_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	400301	SO:0001096	SO:0001092	polypeptide_copper_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	400302	SO:0001097	SO:0001092	polypeptide_iron_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	400303	SO:0001097	SO:0001092	polypeptide_iron_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	400304	SO:0001098	SO:0001092	polypeptide_magnesium_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	400305	SO:0001098	SO:0001092	polypeptide_magnesium_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	400306	SO:0001099	SO:0001092	polypeptide_manganese_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	400307	SO:0001099	SO:0001092	polypeptide_manganese_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	400308	SO:0001100	SO:0001092	polypeptide_molybdenum_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	400309	SO:0001100	SO:0001092	polypeptide_molybdenum_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	400310	SO:0001101	SO:0001092	polypeptide_nickel_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	400311	SO:0001101	SO:0001092	polypeptide_nickel_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	400312	SO:0001102	SO:0001092	polypeptide_tungsten_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	400313	SO:0001102	SO:0001092	polypeptide_tungsten_ion_contact_site	SO:0100002
2	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	biosapiens	metal_binding_site	\N	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	400314	SO:0001103	SO:0001092	polypeptide_zinc_ion_contact_site	SO:0001656
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	biosapiens	molecular_contact_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	400315	SO:0001103	SO:0001092	polypeptide_zinc_ion_contact_site	SO:0100002
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	\N	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	400316	SO:0001104	SO:0001237	catalytic_residue	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	\N	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	400317	SO:0001104	SO:0001237	catalytic_residue	SO:0001411
2	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	400318	SO:0001104	SO:0100019	catalytic_residue	SO:0100001
2	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	400319	SO:0001105	SO:0001657	polypeptide_ligand_contact	SO:0000409
2	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	400320	SO:0001105	SO:0100002	polypeptide_ligand_contact	SO:0100001
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400321	SO:0001106	SO:0001078	asx_motif	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400322	SO:0001107	SO:0001078	beta_bulge	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400323	SO:0001108	SO:0001078	beta_bulge_loop	SO:0001070
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400324	SO:0001109	SO:0001108	beta_bulge_loop_five	SO:0001078
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400325	SO:0001110	SO:0001108	beta_bulge_loop_six	SO:0001078
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	400326	SO:0001111	SO:0001078	beta_strand	SO:0001070
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	400327	SO:0001112	SO:0001111	antiparallel_beta_strand	SO:0001078
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	400328	SO:0001113	SO:0001111	parallel_beta_strand	SO:0001078
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	400329	SO:0001114	SO:0001078	peptide_helix	SO:0001070
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	400330	SO:0001115	SO:0001114	left_handed_peptide_helix	SO:0001078
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	400331	SO:0001116	SO:0001114	right_handed_peptide_helix	SO:0001078
2	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	biosapiens	peptide_helix	biosapiens	biosapiens	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	400332	SO:0001117	SO:0001116	alpha_helix	SO:0001114
2	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	biosapiens	peptide_helix	biosapiens	biosapiens	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	400333	SO:0001118	SO:0001116	pi_helix	SO:0001114
2	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	biosapiens	peptide_helix	biosapiens	biosapiens	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	400334	SO:0001119	SO:0001116	three_ten_helix	SO:0001114
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400335	SO:0001120	SO:0001078	polypeptide_nest_motif	SO:0001070
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400336	SO:0001121	SO:0001120	polypeptide_nest_left_right_motif	SO:0001078
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400337	SO:0001122	SO:0001120	polypeptide_nest_right_left_motif	SO:0001078
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400338	SO:0001123	SO:0001078	schellmann_loop	SO:0001070
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400339	SO:0001124	SO:0001123	schellmann_loop_seven	SO:0001078
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400340	SO:0001125	SO:0001123	schellmann_loop_six	SO:0001078
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400341	SO:0001126	SO:0001078	serine_threonine_motif	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400342	SO:0001127	SO:0001078	serine_threonine_staple_motif	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	400343	SO:0001128	SO:0001078	polypeptide_turn_motif	SO:0001070
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400344	SO:0001129	SO:0000912	asx_turn_left_handed_type_one	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400345	SO:0001130	SO:0000912	asx_turn_left_handed_type_two	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400346	SO:0001131	SO:0000912	asx_turn_right_handed_type_two	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400347	SO:0001132	SO:0000912	asx_turn_right_handed_type_one	SO:0001128
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400348	SO:0001133	SO:0001128	beta_turn	SO:0001078
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400349	SO:0001134	SO:0001133	beta_turn_left_handed_type_one	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400350	SO:0001135	SO:0001133	beta_turn_left_handed_type_two	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400351	SO:0001136	SO:0001133	beta_turn_right_handed_type_one	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400352	SO:0001137	SO:0001133	beta_turn_right_handed_type_two	SO:0001128
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400353	SO:0001138	SO:0001128	gamma_turn	SO:0001078
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400354	SO:0001139	SO:0001138	gamma_turn_classic	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400355	SO:0001140	SO:0001138	gamma_turn_inverse	SO:0001128
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400356	SO:0001141	SO:0001128	serine_threonine_turn	SO:0001078
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400357	SO:0001142	SO:0001141	st_turn_left_handed_type_one	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400358	SO:0001143	SO:0001141	st_turn_left_handed_type_two	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400359	SO:0001144	SO:0001141	st_turn_right_handed_type_one	SO:0001128
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	400360	SO:0001145	SO:0001141	st_turn_right_handed_type_two	SO:0001128
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	SO	400361	SO:0001146	SO:0000839	polypeptide_variation_site	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	SO	400362	SO:0001146	SO:0000839	polypeptide_variation_site	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	SO	400363	SO:0001147	SO:0001146	natural_variant_site	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	SO	400364	SO:0001148	SO:0001146	mutated_variant_site	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	SO	400365	SO:0001149	SO:0001146	alternate_sequence_site	SO:0000839
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	400366	SO:0001150	SO:0001133	beta_turn_type_six	SO:0001128
2	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	400367	SO:0001151	SO:0001150	beta_turn_type_six_a	SO:0001133
2	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	biosapiens	beta_turn_type_six	biosapiens	biosapiens	sequence	"" []	SO	400368	SO:0001152	SO:0001151	beta_turn_type_six_a_one	SO:0001150
2	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	biosapiens	beta_turn_type_six	biosapiens	biosapiens	sequence	"" []	SO	400369	SO:0001153	SO:0001151	beta_turn_type_six_a_two	SO:0001150
2	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	400370	SO:0001154	SO:0001150	beta_turn_type_six_b	SO:0001133
2	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	400371	SO:0001155	SO:0001133	beta_turn_type_eight	SO:0001128
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	400372	SO:0001156	SO:0000713	DRE_motif	SO:0000714
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	400373	SO:0001156	SO:0000170	DRE_motif	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	SO	400374	SO:0001157	SO:0001659	DMv4_motif	SO:0000713
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	400375	SO:0001158	SO:0000713	E_box_motif	SO:0000714
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	400376	SO:0001158	SO:0000170	E_box_motif	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	400377	SO:0001159	SO:0001659	DMv5_motif	SO:0000713
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	400378	SO:0001159	SO:0000170	DMv5_motif	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	400379	SO:0001160	SO:0001659	DMv3_motif	SO:0000713
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	400380	SO:0001160	SO:0000170	DMv3_motif	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	400381	SO:0001161	SO:0001659	DMv2_motif	SO:0000713
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	400382	SO:0001161	SO:0000170	DMv2_motif	SO:0001203
2	"" []	\N	promoter_element	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	400383	SO:0001162	SO:0001660	MTE	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	400384	SO:0001162	SO:0001669	MTE	SO:0000170
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	400385	SO:0001163	SO:0000713	INR1_motif	SO:0000714
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	400386	SO:0001163	SO:0000170	INR1_motif	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	400387	SO:0001164	SO:0001659	DPE1_motif	SO:0000713
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	400388	SO:0001164	SO:0000170	DPE1_motif	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	400389	SO:0001165	SO:0001659	DMv1_motif	SO:0000713
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	400390	SO:0001165	SO:0000170	DMv1_motif	SO:0001203
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	400391	SO:0001166	SO:0000713	GAGA_motif	SO:0000714
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	400392	SO:0001166	SO:0000170	GAGA_motif	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	400393	SO:0001167	SO:0001659	NDM2_motif	SO:0000713
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	400394	SO:0001167	SO:0000170	NDM2_motif	SO:0001203
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	400395	SO:0001168	SO:0001659	NDM3_motif	SO:0000713
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	400396	SO:0001168	SO:0000170	NDM3_motif	SO:0001203
2	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	400397	SO:0001169	SO:0001041	ds_RNA_viral_sequence	SO:0001038
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	400398	SO:0001169	SO:0001041	ds_RNA_viral_sequence	SO:0001235
2	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	400399	SO:0001170	SO:0000208	polinton	SO:0000182
2	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	\N	rRNA	SOFA	SOFA	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	400400	SO:0001171	SO:0000651	rRNA_21S	SO:0000252
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	400401	SO:0001172	SO:0000834	tRNA_region	SO:0000833
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	400402	SO:0001172	SO:0000253	tRNA_region	SO:0000655
2	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	400403	SO:0001173	SO:0001172	anticodon_loop	SO:0000253
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	400404	SO:0001173	SO:0001172	anticodon_loop	SO:0000834
3	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	733288	SO:0001174	SO:0001172	anticodon	SO:0000253
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	733289	SO:0001174	SO:0001172	anticodon	SO:0000834
2	"A region of a tRNA." [RSC:cb]	\N	tRNA_region	\N	\N	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	400407	SO:0001174	SO:0001173	anticodon	SO:0001172
2	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	400408	SO:0001175	SO:0001172	CCA_tail	SO:0000253
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	400409	SO:0001175	SO:0001172	CCA_tail	SO:0000834
2	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	400410	SO:0001176	SO:0001172	DHU_loop	SO:0000253
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	400411	SO:0001176	SO:0001172	DHU_loop	SO:0000834
2	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	\N	tRNA	SOFA	\N	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	400412	SO:0001177	SO:0001172	T_loop	SO:0000253
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	\N	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	400413	SO:0001177	SO:0001172	T_loop	SO:0000834
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	400414	SO:0001178	SO:0000210	pyrrolysine_tRNA_primary_transcript	SO:0000483
2	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	\N	snoRNA	SOFA	SOFA	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	400415	SO:0001179	SO:0000593	U3_snoRNA	SO:0000275
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	400416	SO:0001180	SO:0000837	AU_rich_element	SO:0000836
2	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	400417	SO:0001180	SO:0000205	AU_rich_element	SO:0000203
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	400418	SO:0001181	SO:0000837	Bruno_response_element	SO:0000836
2	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	400419	SO:0001181	SO:0000205	Bruno_response_element	SO:0000203
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	400420	SO:0001182	SO:0000837	iron_responsive_element	SO:0000836
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	400421	SO:0001182	SO:0000203	iron_responsive_element	SO:0000836
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]	SO	400422	SO:0001183	SO:0000348	morpholino_backbone	SO:0000443
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]	SO	400423	SO:0001184	SO:0000348	PNA	SO:0000443
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	400424	SO:0001185	SO:0000733	enzymatic	SO:0000400
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]	SO	400425	SO:0001186	SO:0001185	ribozymic	SO:0000733
2	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	\N	snoRNA	SOFA	\N	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	400426	SO:0001187	SO:0000594	pseudouridylation_guide_snoRNA	SO:0000275
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]	SO	400427	SO:0001188	SO:0000348	LNA	SO:0000443
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"An oligo composed of LNA residues." [RSC:cb]	SO	400428	SO:0001189	SO:0001247	LNA_oligo	SO:0000696
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]	SO	400429	SO:0001190	SO:0000348	TNA	SO:0000443
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"An oligo composed of TNA residues." [RSC:cb]	SO	400430	SO:0001191	SO:0001247	TNA_oligo	SO:0000696
2	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]	SO	400431	SO:0001192	SO:0000348	GNA	SO:0000443
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"An oligo composed of GNA residues." [RSC:cb]	SO	400432	SO:0001193	SO:0001247	GNA_oligo	SO:0000696
2	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]	SO	400433	SO:0001194	SO:0001192	R_GNA	SO:0000348
2	"An oligo composed of synthetic nucleotides." [SO:ke]	\N	synthetic_oligo	\N	\N	sequence	"An oligo composed of (R)-GNA residues." [RSC:cb]	SO	400434	SO:0001195	SO:0001193	R_GNA_oligo	SO:0001247
2	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]	SO	400435	SO:0001196	SO:0001192	S_GNA	SO:0000348
2	"An oligo composed of synthetic nucleotides." [SO:ke]	\N	synthetic_oligo	\N	\N	sequence	"An oligo composed of (S)-GNA residues." [RSC:cb]	SO	400436	SO:0001197	SO:0001193	S_GNA_oligo	SO:0001247
2	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	400437	SO:0001198	SO:0001041	ds_DNA_viral_sequence	SO:0001038
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	400438	SO:0001198	SO:0001041	ds_DNA_viral_sequence	SO:0001235
2	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	400439	SO:0001199	SO:0001041	ss_RNA_viral_sequence	SO:0001038
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	400440	SO:0001199	SO:0001041	ss_RNA_viral_sequence	SO:0001235
2	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	400441	SO:0001200	SO:0001199	negative_sense_ssRNA_viral_sequence	SO:0001041
2	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	400442	SO:0001201	SO:0001199	positive_sense_ssRNA_viral_sequence	SO:0001041
2	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	\N	viral_sequence	\N	\N	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	400443	SO:0001202	SO:0001199	ambisense_ssRNA_viral_sequence	SO:0001041
2	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	400444	SO:0001203	SO:0000167	RNA_polymerase_promoter	SO:0001055
2	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	400445	SO:0001204	SO:0001203	Phage_RNA_Polymerase_Promoter	SO:0000167
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	400446	SO:0001205	SO:0001204	SP6_RNA_Polymerase_Promoter	SO:0001203
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	400447	SO:0001206	SO:0001204	T3_RNA_Polymerase_Promoter	SO:0001203
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	400448	SO:0001207	SO:0001204	T7_RNA_Polymerase_Promoter	SO:0001203
2	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	SOFA	sequence	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	400449	SO:0001208	SO:0000345	five_prime_EST	SO:0000324
2	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	SOFA	sequence	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	400450	SO:0001209	SO:0000345	three_prime_EST	SO:0000324
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	400451	SO:0001210	SO:0000836	translational_frameshift	SO:0000234
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	400452	SO:0001210	SO:0000836	translational_frameshift	SO:0000834
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	400453	SO:0001211	SO:0001210	plus_1_translational_frameshift	SO:0000836
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	400454	SO:0001212	SO:0001210	plus_2_translational_frameshift	SO:0000836
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	400455	SO:0001213	SO:0000588	group_III_intron	SO:0000188
2	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	400456	SO:0001214	SO:0000852	noncoding_region_of_exon	SO:0000147
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	400457	SO:0001214	SO:0000852	noncoding_region_of_exon	SO:0000833
2	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	400458	SO:0001215	SO:0000852	coding_region_of_exon	SO:0000147
2	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	400459	SO:0001215	SO:0000852	coding_region_of_exon	SO:0000833
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	400460	SO:0001216	SO:0000188	endonuclease_spliced_intron	SO:0000835
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	400461	SO:0001217	SO:0000704	protein_coding_gene	SO:0001411
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]	SO	400462	SO:0001218	SO:0000667	transgenic_insertion	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	DBVAR,SOFA	sequence	"An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]	SO	400463	SO:0001218	SO:0000667	transgenic_insertion	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	400464	SO:0001219	SO:0000704	retrogene	SO:0001411
2	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	SO	400465	SO:0001220	SO:0000893	silenced_by_RNA_interference	SO:0000126
2	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	SO	400466	SO:0001221	SO:0000893	silenced_by_histone_modification	SO:0000126
2	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	\N	silenced	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	400467	SO:0001222	SO:0001221	silenced_by_histone_methylation	SO:0000893
2	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	\N	silenced	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	400468	SO:0001223	SO:0001221	silenced_by_histone_deacetylation	SO:0000893
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced by RNA interference." [SO:xp]	SO	400469	SO:0001224	SO:0000127	gene_silenced_by_RNA_interference	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced by histone modification." [SO:xp]	SO	400470	SO:0001225	SO:0000127	gene_silenced_by_histone_modification	SO:0000704
2	"A gene that is silenced." [SO:xp]	\N	silenced_gene	\N	\N	sequence	"A gene that is silenced by histone methylation." [SO:xp]	SO	400471	SO:0001226	SO:0001225	gene_silenced_by_histone_methylation	SO:0000127
2	"A gene that is silenced." [SO:xp]	\N	silenced_gene	\N	\N	sequence	"A gene that is silenced by histone deacetylation." [SO:xp]	SO	400472	SO:0001227	SO:0001225	gene_silenced_by_histone_deacetylation	SO:0000127
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]	SO	400473	SO:0001228	SO:0001277	dihydrouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]	SO	400474	SO:0001229	SO:0001277	pseudouridine	SO:0000250
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	SO	400475	SO:0001230	SO:0000250	inosine	SO:0001236
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]	SO	400476	SO:0001231	SO:0000250	seven_methylguanine	SO:0001236
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]	SO	400477	SO:0001232	SO:0000250	ribothymidine	SO:0001236
2	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	\N	inosine	\N	\N	sequence	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	SO	400478	SO:0001233	SO:0001274	methylinosine	SO:0001230
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb]	SO	400479	SO:0001234	SO:0000733	mobile	SO:0000400
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SO	400480	SO:0001235	SO:0001411	replicon	SO:0000001
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SO	400481	SO:0001236	SO:0001411	base	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	SO	733373	SO:0001237	SO:0001411	amino_acid	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	SO	400483	SO:0001237	SO:0000104	amino_acid	SO:0001411
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"" []	SO	400484	SO:0001238	SO:0000315	major_TSS	SO:0000835
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"" []	SO	400485	SO:0001239	SO:0000315	minor_TSS	SO:0000835
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	SOFA	sequence	"The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]	SO	400486	SO:0001240	SO:0000842	TSS_region	SO:0000704
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]	SO	400487	SO:0001240	SO:0000842	TSS_region	SO:0001411
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400488	SO:0001241	SO:0000401	encodes_alternate_transcription_start_sites	SO:0000733
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	400489	SO:0001243	SO:0000835	miRNA_primary_transcript_region	SO:0000185
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	400490	SO:0001243	SO:0000835	miRNA_primary_transcript_region	SO:0000833
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	400491	SO:0001244	SO:0001243	pre_miRNA	SO:0000835
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	400492	SO:0001244	SO:0000647	pre_miRNA	SO:0000483
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	733390	SO:0001245	SO:0001243	miRNA_stem	SO:0000835
2	"A primary transcript encoding a micro RNA." [SO:ke]	\N	miRNA_primary_transcript	\N	\N	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	400494	SO:0001245	SO:0001244	miRNA_stem	SO:0000647
2	"A part of an miRNA primary_transcript." [SO:ke]	\N	miRNA_primary_transcript_region	\N	\N	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	400495	SO:0001245	SO:0001244	miRNA_stem	SO:0001243
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	733394	SO:0001246	SO:0001243	miRNA_loop	SO:0000835
2	"A primary transcript encoding a micro RNA." [SO:ke]	\N	miRNA_primary_transcript	\N	\N	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	400497	SO:0001246	SO:0001244	miRNA_loop	SO:0000647
2	"A part of an miRNA primary_transcript." [SO:ke]	\N	miRNA_primary_transcript_region	\N	\N	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	400498	SO:0001246	SO:0001244	miRNA_loop	SO:0001243
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An oligo composed of synthetic nucleotides." [SO:ke]	SO	400499	SO:0001247	SO:0000696	synthetic_oligo	SO:0000695
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SO	400500	SO:0001248	SO:0001410	assembly	SO:0000001
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	SO	400501	SO:0001249	SO:0001248	fragment_assembly	SO:0001410
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	\N	sequence	"A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]	SO	400502	SO:0001250	SO:0001249	fingerprint_map	SO:0001248
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	\N	sequence	"An STS map is a physical map organized by the unique STS landmarks." [SO:ke]	SO	400503	SO:0001251	SO:0001249	STS_map	SO:0001248
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	\N	sequence	"A radiation hybrid map is a physical map." [SO:ke]	SO	400504	SO:0001252	SO:0001249	RH_map	SO:0001248
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]	SO	400505	SO:0001253	SO:0000143	sonicate_fragment	SO:0001410
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	400506	SO:0001254	SO:1000182	polyploid	SO:0000240
2	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	chromosome_number_variation	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	400507	SO:0001255	SO:0001254	autopolyploid	SO:1000182
2	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	\N	chromosome_number_variation	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	400508	SO:0001256	SO:0001254	allopolyploid	SO:1000182
2	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	nucleotide_to_protein_binding_site	SOFA	SOFA	sequence	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	SO	400509	SO:0001257	SO:0000059	homing_endonuclease_binding_site	SO:0001654
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	400510	SO:0001258	SO:0000713	octamer_motif	SO:0000714
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	400511	SO:0001258	SO:0000170	octamer_motif	SO:0001203
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A chromosome originating in an apicoplast." [SO:xp]	SO	400512	SO:0001259	SO:0000340	apicoplast_chromosome	SO:0001235
2	"A comment about the sequence." [SO:ke]	\N	remark	SOFA	SOFA	sequence	"A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]	SO	400513	SO:0001261	SO:0000703	overlapping_feature_set	SO:0000700
2	"A region of sequence implicated in an experimental result." [SO:ke]	\N	experimental_result_region	SOFA	\N	sequence	"A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]	SO	400514	SO:0001262	SO:0001261	overlapping_EST_set	SO:0000703
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	400515	SO:0001263	SO:0000704	ncRNA_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400516	SO:0001264	SO:0001263	gRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400517	SO:0001265	SO:0001263	miRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400518	SO:0001266	SO:0001263	scRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400519	SO:0001267	SO:0001263	snoRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400520	SO:0001268	SO:0001263	snRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400521	SO:0001269	SO:0001263	SRP_RNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400522	SO:0001270	SO:0001263	stRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400523	SO:0001271	SO:0001263	tmRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	400524	SO:0001272	SO:0001263	tRNA_gene	SO:0000704
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	SO	400525	SO:0001273	SO:0000250	modified_adenosine	SO:0001236
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	SO	400526	SO:0001274	SO:0001230	modified_inosine	SO:0000250
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	SO	400527	SO:0001275	SO:0000250	modified_cytidine	SO:0001236
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"" []	SO	400528	SO:0001276	SO:0000250	modified_guanosine	SO:0001236
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"" []	SO	400529	SO:0001277	SO:0000250	modified_uridine	SO:0001236
2	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	\N	inosine	\N	\N	sequence	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	400530	SO:0001278	SO:0001274	one_methylinosine	SO:0001230
2	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	\N	inosine	\N	\N	sequence	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	400531	SO:0001279	SO:0001274	one_two_prime_O_dimethylinosine	SO:0001230
2	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	\N	inosine	\N	\N	sequence	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	400532	SO:0001280	SO:0001274	two_prime_O_methylinosine	SO:0001230
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400533	SO:0001281	SO:0001275	three_methylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400534	SO:0001282	SO:0001275	five_methylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400535	SO:0001283	SO:0001275	two_prime_O_methylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400536	SO:0001284	SO:0001275	two_thiocytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400537	SO:0001285	SO:0001275	N4_acetylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400538	SO:0001286	SO:0001275	five_formylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400539	SO:0001287	SO:0001275	five_two_prime_O_dimethylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400540	SO:0001288	SO:0001275	N4_acetyl_2_prime_O_methylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400541	SO:0001289	SO:0001275	lysidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400542	SO:0001290	SO:0001275	N4_methylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400543	SO:0001291	SO:0001275	N4_2_prime_O_dimethylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400544	SO:0001292	SO:0001275	five_hydroxymethylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400545	SO:0001293	SO:0001275	five_formyl_two_prime_O_methylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	400546	SO:0001294	SO:0001275	N4_N4_2_prime_O_trimethylcytidine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400547	SO:0001295	SO:0001273	one_methyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400548	SO:0001296	SO:0001273	two_methyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400549	SO:0001297	SO:0001273	N6_methyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400550	SO:0001298	SO:0001273	two_prime_O_methyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400551	SO:0001299	SO:0001273	two_methylthio_N6_methyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400552	SO:0001300	SO:0001273	N6_isopentenyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400553	SO:0001301	SO:0001273	two_methylthio_N6_isopentenyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400554	SO:0001302	SO:0001273	N6_cis_hydroxyisopentenyl_adenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400555	SO:0001303	SO:0001273	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400556	SO:0001304	SO:0001273	N6_glycinylcarbamoyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400557	SO:0001305	SO:0001273	N6_threonylcarbamoyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400558	SO:0001306	SO:0001273	two_methylthio_N6_threonyl_carbamoyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400559	SO:0001307	SO:0001273	N6_methyl_N6_threonylcarbamoyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400560	SO:0001308	SO:0001273	N6_hydroxynorvalylcarbamoyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400561	SO:0001309	SO:0001273	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400562	SO:0001310	SO:0001273	two_prime_O_ribosyladenosine_phosphate	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400563	SO:0001311	SO:0001273	N6_N6_dimethyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400564	SO:0001312	SO:0001273	N6_2_prime_O_dimethyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400565	SO:0001313	SO:0001273	N6_N6_2_prime_O_trimethyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400566	SO:0001314	SO:0001273	one_two_prime_O_dimethyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	400567	SO:0001315	SO:0001273	N6_acetyladenosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	SO	400568	SO:0001316	SO:0001276	seven_deazaguanosine	SO:0000250
2	"" []	\N	modified_guanosine	\N	\N	sequence	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	400569	SO:0001317	SO:0001316	queuosine	SO:0001276
2	"" []	\N	modified_guanosine	\N	\N	sequence	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	400570	SO:0001318	SO:0001316	epoxyqueuosine	SO:0001276
2	"" []	\N	modified_guanosine	\N	\N	sequence	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	400571	SO:0001319	SO:0001316	galactosyl_queuosine	SO:0001276
2	"" []	\N	modified_guanosine	\N	\N	sequence	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	400572	SO:0001320	SO:0001316	mannosyl_queuosine	SO:0001276
2	"" []	\N	modified_guanosine	\N	\N	sequence	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	400573	SO:0001321	SO:0001316	seven_cyano_seven_deazaguanosine	SO:0001276
2	"" []	\N	modified_guanosine	\N	\N	sequence	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	400574	SO:0001322	SO:0001316	seven_aminomethyl_seven_deazaguanosine	SO:0001276
2	"" []	\N	modified_guanosine	\N	\N	sequence	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	400575	SO:0001323	SO:0001316	archaeosine	SO:0001276
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400576	SO:0001324	SO:0001276	one_methylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400577	SO:0001325	SO:0001276	N2_methylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400578	SO:0001326	SO:0001276	seven_methylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400579	SO:0001327	SO:0001276	two_prime_O_methylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400580	SO:0001328	SO:0001276	N2_N2_dimethylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400581	SO:0001329	SO:0001276	N2_2_prime_O_dimethylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400582	SO:0001330	SO:0001276	N2_N2_2_prime_O_trimethylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400583	SO:0001331	SO:0001276	two_prime_O_ribosylguanosine_phosphate	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400584	SO:0001332	SO:0001276	wybutosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400585	SO:0001333	SO:0001276	peroxywybutosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400586	SO:0001334	SO:0001276	hydroxywybutosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400587	SO:0001335	SO:0001276	undermodified_hydroxywybutosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400588	SO:0001336	SO:0001276	wyosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400589	SO:0001337	SO:0001276	methylwyosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400590	SO:0001338	SO:0001276	N2_7_dimethylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400591	SO:0001339	SO:0001276	N2_N2_7_trimethylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400592	SO:0001340	SO:0001276	one_two_prime_O_dimethylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400593	SO:0001341	SO:0001276	four_demethylwyosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400594	SO:0001342	SO:0001276	isowyosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400595	SO:0001343	SO:0001276	N2_7_2prirme_O_trimethylguanosine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400596	SO:0001344	SO:0001277	five_methyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400597	SO:0001345	SO:0001277	two_prime_O_methyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400598	SO:0001346	SO:0001277	five_two_prime_O_dimethyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400599	SO:0001347	SO:0001277	one_methylpseudouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400600	SO:0001348	SO:0001277	two_prime_O_methylpseudouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400601	SO:0001349	SO:0001277	two_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400602	SO:0001350	SO:0001277	four_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400603	SO:0001351	SO:0001277	five_methyl_2_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400604	SO:0001352	SO:0001277	two_thio_two_prime_O_methyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400605	SO:0001353	SO:0001277	three_three_amino_three_carboxypropyl_uridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400606	SO:0001354	SO:0001277	five_hydroxyuridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400607	SO:0001355	SO:0001277	five_methoxyuridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400608	SO:0001356	SO:0001277	uridine_five_oxyacetic_acid	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400609	SO:0001357	SO:0001277	uridine_five_oxyacetic_acid_methyl_ester	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400610	SO:0001358	SO:0001277	five_carboxyhydroxymethyl_uridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400611	SO:0001359	SO:0001277	five_carboxyhydroxymethyl_uridine_methyl_ester	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400612	SO:0001360	SO:0001277	five_methoxycarbonylmethyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400613	SO:0001361	SO:0001277	five_methoxycarbonylmethyl_two_prime_O_methyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400614	SO:0001362	SO:0001277	five_methoxycarbonylmethyl_two_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400615	SO:0001363	SO:0001277	five_aminomethyl_two_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400616	SO:0001364	SO:0001277	five_methylaminomethyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400617	SO:0001365	SO:0001277	five_methylaminomethyl_two_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400618	SO:0001366	SO:0001277	five_methylaminomethyl_two_selenouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400619	SO:0001367	SO:0001277	five_carbamoylmethyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400620	SO:0001368	SO:0001277	five_carbamoylmethyl_two_prime_O_methyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400621	SO:0001369	SO:0001277	five_carboxymethylaminomethyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400622	SO:0001370	SO:0001277	five_carboxymethylaminomethyl_two_prime_O_methyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400623	SO:0001371	SO:0001277	five_carboxymethylaminomethyl_two_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400624	SO:0001372	SO:0001277	three_methyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400625	SO:0001373	SO:0001277	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400626	SO:0001374	SO:0001277	five_carboxymethyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400627	SO:0001375	SO:0001277	three_two_prime_O_dimethyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400628	SO:0001376	SO:0001277	five_methyldihydrouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400629	SO:0001377	SO:0001277	three_methylpseudouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400630	SO:0001378	SO:0001277	five_taurinomethyluridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400631	SO:0001379	SO:0001277	five_taurinomethyl_two_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400632	SO:0001380	SO:0001277	five_isopentenylaminomethyl_uridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400633	SO:0001381	SO:0001277	five_isopentenylaminomethyl_two_thiouridine	SO:0000250
2	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	400634	SO:0001382	SO:0001277	five_isopentenylaminomethyl_two_prime_O_methyluridine	SO:0000250
2	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]	SO	400635	SO:0001383	SO:0001654	histone_binding_site	SO:0000410
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"" []	SO	400636	SO:0001384	SO:0000316	CDS_fragment	SO:0000836
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified amino acid feature." [SO:ke]	SO	400637	SO:0001385	SO:0001237	modified_amino_acid_feature	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified amino acid feature." [SO:ke]	SO	400638	SO:0001385	SO:0001237	modified_amino_acid_feature	SO:0001411
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified glycine amino acid feature." [SO:ke]	SO	400639	SO:0001386	SO:0001385	modified_glycine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified alanine amino acid feature." [SO:ke]	SO	400640	SO:0001387	SO:0001385	modified_L_alanine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified asparagine amino acid feature." [SO:ke]	SO	400641	SO:0001388	SO:0001385	modified_L_asparagine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	SO	400642	SO:0001389	SO:0001385	modified_L_aspartic_acid	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified cysteine amino acid feature." [SO:ke]	SO	400643	SO:0001390	SO:0001385	modified_L_cysteine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"" []	SO	400644	SO:0001391	SO:0001385	modified_L_glutamic_acid	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified threonine amino acid feature." [SO:ke]	SO	400645	SO:0001392	SO:0001385	modified_L_threonine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified tryptophan amino acid feature." [SO:ke]	SO	400646	SO:0001393	SO:0001385	modified_L_tryptophan	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified glutamine amino acid feature." [SO:ke]	SO	400647	SO:0001394	SO:0001385	modified_L_glutamine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified methionine amino acid feature." [SO:ke]	SO	400648	SO:0001395	SO:0001385	modified_L_methionine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified isoleucine amino acid feature." [SO:ke]	SO	400649	SO:0001396	SO:0001385	modified_L_isoleucine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	SO	400650	SO:0001397	SO:0001385	modified_L_phenylalanine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified histidine amino acid feature." [SO:ke]	SO	400651	SO:0001398	SO:0001385	modified_L_histidine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified serine amino acid feature." [SO:ke]	SO	400652	SO:0001399	SO:0001385	modified_L_serine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified lysine amino acid feature." [SO:ke]	SO	400653	SO:0001400	SO:0001385	modified_L_lysine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified leucine amino acid feature." [SO:ke]	SO	400654	SO:0001401	SO:0001385	modified_L_leucine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	SO	400655	SO:0001402	SO:0001385	modified_L_selenocysteine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified valine amino acid feature." [SO:ke]	SO	400656	SO:0001403	SO:0001385	modified_L_valine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified proline amino acid feature." [SO:ke]	SO	400657	SO:0001404	SO:0001385	modified_L_proline	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified tyrosine amino acid feature." [SO:ke]	SO	400658	SO:0001405	SO:0001385	modified_L_tyrosine	SO:0001237
2	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	\N	amino_acid	\N	\N	sequence	"A post translationally modified arginine amino acid feature." [SO:ke]	SO	400659	SO:0001406	SO:0001385	modified_L_arginine	SO:0001237
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke]	SO	400660	SO:0001407	SO:0000443	peptidyl	SO:0000400
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	400661	SO:0001408	SO:0100011	cleaved_for_gpi_anchor_region	SO:0000839
2	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	\N	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	400662	SO:0001408	SO:0100011	cleaved_for_gpi_anchor_region	SO:0001063
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region which is intended for use in an experiment." [SO:cb]	SO	400663	SO:0001409	SO:0000001	biomaterial_region	SO:0000110
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SO	400664	SO:0001410	SO:0000001	experimental_feature	SO:0000110
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SO	400665	SO:0001411	SO:0000001	biological_region	SO:0000110
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	SO	400666	SO:0001412	SO:0000001	topologically_defined_region	SO:0000110
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	400667	SO:0001413	SO:0001021	translocation_breakpoint	SO:0000340
2	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	400668	SO:0001413	SO:0001021	translocation_breakpoint	SO:0000699
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	400669	SO:0001414	SO:0001021	insertion_breakpoint	SO:0000340
2	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	400670	SO:0001414	SO:0001021	insertion_breakpoint	SO:0000699
2	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	400671	SO:0001415	SO:0001021	deletion_breakpoint	SO:0000340
2	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	400672	SO:0001415	SO:0001021	deletion_breakpoint	SO:0000699
2	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	SOFA	sequence	"A flanking region located five prime of a specific region." [SO:chado]	SO	400673	SO:0001416	SO:0000239	five_prime_flanking_region	SO:0001412
2	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	SOFA	sequence	"A flanking region located three prime of a specific region." [SO:chado]	SO	400674	SO:0001417	SO:0000239	three_prime_flanking_region	SO:0001412
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]	SO	400675	SO:0001418	SO:0001410	transcribed_fragment	SO:0000001
2	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	400676	SO:0001419	SO:0000162	cis_splice_site	SO:0000835
2	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	400677	SO:0001420	SO:0000162	trans_splice_site	SO:0000835
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The boundary between an intron and an exon." [SO:ke]	SO	400678	SO:0001421	SO:0000699	splice_junction	SO:0000110
2	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	400679	SO:0001422	SO:0100001	conformational_switch	SO:0001067
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	400680	SO:0001423	SO:0000150	dye_terminator_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	400681	SO:0001423	SO:0000150	dye_terminator_read	SO:0000149
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	400682	SO:0001424	SO:0000150	pyrosequenced_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	400683	SO:0001424	SO:0000150	pyrosequenced_read	SO:0000149
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	400684	SO:0001425	SO:0000150	ligation_based_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	400685	SO:0001425	SO:0000150	ligation_based_read	SO:0000149
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	400686	SO:0001426	SO:0000150	polymerase_synthesis_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	400687	SO:0001426	SO:0000150	polymerase_synthesis_read	SO:0000149
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]	SO	400688	SO:0001427	SO:0001679	cis_regulatory_frameshift_element	SO:0005836
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A sequence assembly derived from expressed sequences." [SO:ke]	SO	400689	SO:0001428	SO:0000353	expressed_sequence_assembly	SO:0001248
2	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	SO	400690	SO:0001429	SO:0001655	DNA_binding_site	SO:0000409
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]	SO	400691	SO:0001431	SO:0000704	cryptic_gene	SO:0001411
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]	SO	400692	SO:0001433	SO:0000317	three_prime_RACE_clone	SO:0000151
2	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]	SO	400693	SO:0001434	SO:0001760	cassette_pseudogene	SO:0000336
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400694	SO:0001435	SO:0001237	alanine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400695	SO:0001435	SO:0001237	alanine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400696	SO:0001436	SO:0001237	valine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400697	SO:0001436	SO:0001237	valine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400698	SO:0001437	SO:0001237	leucine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400699	SO:0001437	SO:0001237	leucine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400700	SO:0001438	SO:0001237	isoleucine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400701	SO:0001438	SO:0001237	isoleucine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400702	SO:0001439	SO:0001237	proline	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400703	SO:0001439	SO:0001237	proline	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400704	SO:0001440	SO:0001237	tryptophan	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400705	SO:0001440	SO:0001237	tryptophan	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400706	SO:0001441	SO:0001237	phenylalanine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400707	SO:0001441	SO:0001237	phenylalanine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400708	SO:0001442	SO:0001237	methionine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400709	SO:0001442	SO:0001237	methionine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400710	SO:0001443	SO:0001237	glycine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400711	SO:0001443	SO:0001237	glycine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400712	SO:0001444	SO:0001237	serine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400713	SO:0001444	SO:0001237	serine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400714	SO:0001445	SO:0001237	threonine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400715	SO:0001445	SO:0001237	threonine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400716	SO:0001446	SO:0001237	tyrosine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400717	SO:0001446	SO:0001237	tyrosine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400718	SO:0001447	SO:0001237	cysteine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400719	SO:0001447	SO:0001237	cysteine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400720	SO:0001448	SO:0001237	glutamine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400721	SO:0001448	SO:0001237	glutamine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400722	SO:0001449	SO:0001237	asparagine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400723	SO:0001449	SO:0001237	asparagine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400724	SO:0001450	SO:0001237	lysine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400725	SO:0001450	SO:0001237	lysine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400726	SO:0001451	SO:0001237	arginine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400727	SO:0001451	SO:0001237	arginine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400728	SO:0001452	SO:0001237	histidine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400729	SO:0001452	SO:0001237	histidine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400730	SO:0001453	SO:0001237	aspartic_acid	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400731	SO:0001453	SO:0001237	aspartic_acid	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400732	SO:0001454	SO:0001237	glutamic_acid	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400733	SO:0001454	SO:0001237	glutamic_acid	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400734	SO:0001455	SO:0001237	selenocysteine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400735	SO:0001455	SO:0001237	selenocysteine	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	400736	SO:0001456	SO:0001237	pyrrolysine	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	400737	SO:0001456	SO:0001237	pyrrolysine	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]	SO	400738	SO:0001457	SO:0001410	transcribed_cluster	SO:0000001
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]	SO	400739	SO:0001458	SO:0001457	unigene_cluster	SO:0001410
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]	SO	400740	SO:0001459	SO:0000314	CRISPR	SO:0000657
2	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	400741	SO:0001460	SO:0001654	insulator_binding_site	SO:0000410
2	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	400742	SO:0001460	SO:0000627	insulator_binding_site	SO:0001055
2	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	400743	SO:0001461	SO:0001654	enhancer_binding_site	SO:0000410
2	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	\N	CRM	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	400744	SO:0001461	SO:0000165	enhancer_binding_site	SO:0000727
2	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	\N	polypeptide_sequencing_information	biosapiens	biosapiens	sequence	"A collection of contigs." [SO:ke]	SO	400745	SO:0001462	SO:0001085	contig_collection	SO:0001082
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	400746	SO:0001463	SO:0001877	lincRNA	SO:0000655
2	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	SOFA	sequence	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	SO	400747	SO:0001464	SO:0000345	UST	SO:0000324
2	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	\N	EST	SOFA	\N	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	400748	SO:0001465	SO:0001464	three_prime_UST	SO:0000345
2	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	\N	EST	SOFA	\N	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	400749	SO:0001466	SO:0001464	five_prime_UST	SO:0000345
2	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	400750	SO:0001467	SO:0000345	RST	SO:0000324
2	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	\N	EST	SOFA	\N	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	400751	SO:0001468	SO:0001467	three_prime_RST	SO:0000345
2	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	\N	EST	SOFA	\N	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	400752	SO:0001469	SO:0001467	five_prime_RST	SO:0000345
2	"A match against a nucleotide sequence." [SO:ke]	\N	nucleotide_match	SOFA	SOFA	sequence	"A match against an UST sequence." [SO:nlw]	SO	400753	SO:0001470	SO:0000102	UST_match	SO:0000347
2	"A match against a nucleotide sequence." [SO:ke]	\N	nucleotide_match	SOFA	SOFA	sequence	"A match against an RST sequence." [SO:nlw]	SO	400754	SO:0001471	SO:0000102	RST_match	SO:0000347
2	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	\N	match	SOFA	SOFA	sequence	"A nucleotide match to a primer sequence." [SO:nlw]	SO	400755	SO:0001472	SO:0000347	primer_match	SO:0000343
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	400756	SO:0001473	SO:0001243	miRNA_antiguide	SO:0000835
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The boundary between the spliced leader and the first exon of the mRNA." [SO:ke]	SO	400757	SO:0001474	SO:0000699	trans_splice_junction	SO:0000110
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	400758	SO:0001475	SO:0000835	outron	SO:0000185
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	400759	SO:0001475	SO:0000835	outron	SO:0000833
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	400760	SO:0001476	SO:0000155	natural_plasmid	SO:0001235
2	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	400761	SO:0001476	SO:0001038	natural_plasmid	SO:0001037
2	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	400762	SO:0001477	SO:0000637	gene_trap_construct	SO:0000155
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	400763	SO:0001477	SO:0000637	gene_trap_construct	SO:0000804
2	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	400764	SO:0001478	SO:0000637	promoter_trap_construct	SO:0000155
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	400765	SO:0001478	SO:0000637	promoter_trap_construct	SO:0000804
2	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	\N	plasmid	\N	\N	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	400766	SO:0001479	SO:0000637	enhancer_trap_construct	SO:0000155
2	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	400767	SO:0001479	SO:0000637	enhancer_trap_construct	SO:0000804
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	400768	SO:0001480	SO:0000150	PAC_end	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	400769	SO:0001480	SO:0000150	PAC_end	SO:0000149
2	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	400770	SO:0001480	SO:0000154	PAC_end	SO:0000440
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]	SO	400771	SO:0001481	SO:0000006	RAPD	SO:0000695
2	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	\N	CRM	SOFA	SOFA	sequence	"" []	SO	400772	SO:0001482	SO:0000165	shadow_enhancer	SO:0000727
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SOFA	sequence_alteration	SOFA	SOFA	sequence	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SO	400773	SO:0001483	SO:1000002	SNV	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SO	400774	SO:0001483	SO:1000002	SNV	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	400775	SO:0001484	SO:0000657	X_element_combinatorial_repeat	SO:0001411
2	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	400776	SO:0001484	SO:0000624	X_element_combinatorial_repeat	SO:0000628
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	400777	SO:0001485	SO:0000657	Y_prime_element	SO:0001411
2	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	400778	SO:0001485	SO:0000624	Y_prime_element	SO:0000628
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]	SO	400779	SO:0001486	SO:0001499	standard_draft	SO:0000905
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]	SO	400780	SO:0001487	SO:0001499	high_quality_draft	SO:0000905
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]	SO	400781	SO:0001488	SO:0001499	improved_high_quality_draft	SO:0000905
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]	SO	400782	SO:0001489	SO:0001499	annotation_directed_improved_draft	SO:0000905
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]	SO	400783	SO:0001490	SO:0001499	noncontiguous_finished	SO:0000905
2	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]	SO	400784	SO:0001491	SO:0001499	finished_genome	SO:0000905
2	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	400785	SO:0001492	SO:0001679	intronic_regulatory_region	SO:0005836
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	400786	SO:0001492	SO:0000188	intronic_regulatory_region	SO:0000835
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	400787	SO:0001493	SO:0000330	centromere_DNA_Element_I	SO:0001410
2	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	400788	SO:0001493	SO:0001794	centromere_DNA_Element_I	SO:0000577
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	400789	SO:0001494	SO:0000330	centromere_DNA_Element_II	SO:0001410
2	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	400790	SO:0001494	SO:0001794	centromere_DNA_Element_II	SO:0000577
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	400791	SO:0001495	SO:0000330	centromere_DNA_Element_III	SO:0001410
2	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	400792	SO:0001495	SO:0001794	centromere_DNA_Element_III	SO:0000577
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	400793	SO:0001496	SO:0000657	telomeric_repeat	SO:0001411
2	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	400794	SO:0001496	SO:0000624	telomeric_repeat	SO:0000628
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	400795	SO:0001497	SO:0000330	X_element	SO:0001410
2	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	400796	SO:0001497	SO:0000624	X_element	SO:0000628
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	400797	SO:0001498	SO:0000150	YAC_end	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	400798	SO:0001498	SO:0000150	YAC_end	SO:0000149
2	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	400799	SO:0001498	SO:0000152	YAC_end	SO:0000440
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The status of whole genome sequence." [DOI:10.1126]	SO	400800	SO:0001499	SO:0000905	whole_genome_sequence_status	SO:0000733
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]	SO	400801	SO:0001500	SO:0001645	heritable_phenotypic_marker	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An experimental feature with high sequence identity to another sequence." [SO:ke]	SO	400802	SO:0001502	SO:0001410	high_identity_region	SO:0000001
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]	SO	400803	SO:0001503	SO:0000673	processed_transcript	SO:0000831
2	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome variation derived from an event during meiosis." [SO:ke]	SO	400804	SO:0001504	SO:0000240	assortment_derived_variation	SO:0001507
2	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome variation derived from an event during meiosis." [SO:ke]	SO	400805	SO:0001504	SO:0000240	assortment_derived_variation	SO:0001524
2	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke]	SO	400806	SO:0001505	SO:0001026	reference_genome	SO:0001260
2	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	SO	400807	SO:0001506	SO:0001026	variant_genome	SO:0001260
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	400808	SO:0001508	SO:0000733	alteration_attribute	SO:0000400
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400809	SO:0001509	SO:0001508	chromosomal_variation_attribute	SO:0000733
2	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	400810	SO:0001510	SO:0001509	intrachromosomal	SO:0001508
2	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	400811	SO:0001511	SO:0001509	interchromosomal	SO:0001508
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A quality of a chromosomal insertion,." [SO:ke]	SO	400812	SO:0001512	SO:0001508	insertion_attribute	SO:0000733
2	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	400813	SO:0001513	SO:0001512	tandem	SO:0001508
2	"" []	\N	alteration_attribute	\N	\N	sequence	"A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]	SO	400814	SO:0001514	SO:0001512	direct	SO:0001508
2	"" []	\N	alteration_attribute	\N	\N	sequence	"A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]	SO	400815	SO:0001515	SO:0001512	inverted	SO:0001508
2	"" []	\N	alteration_attribute	\N	\N	sequence	"The quality of a duplication where the new region exists independently of the original." [SO:ke]	SO	400816	SO:0001516	SO:0001523	free	SO:0001508
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400817	SO:0001517	SO:0001508	inversion_attribute	SO:0000733
2	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	400818	SO:0001518	SO:0001517	pericentric	SO:0001508
2	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	400819	SO:0001519	SO:0001517	paracentric	SO:0001508
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400820	SO:0001520	SO:0001508	translocaton_attribute	SO:0000733
2	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	400821	SO:0001521	SO:0001520	reciprocal	SO:0001508
2	"" []	\N	alteration_attribute	\N	\N	sequence	"" []	SO	400822	SO:0001522	SO:0001520	insertional	SO:0001508
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	400823	SO:0001523	SO:0001508	duplication_attribute	SO:0000733
2	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"" []	SO	400824	SO:0001524	SO:0001506	chromosomally_aberrant_genome	SO:0001026
2	"A comment about the sequence." [SO:ke]	\N	remark	SOFA	SOFA	sequence	"A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]	SO	400825	SO:0001525	SO:0000413	assembly_error_correction	SO:0000700
2	"A comment about the sequence." [SO:ke]	\N	remark	SOFA	SOFA	sequence	"A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]	SO	400826	SO:0001526	SO:0000413	base_call_error_correction	SO:0000700
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	SOFA	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	SO	400827	SO:0001527	SO:0000839	peptide_localization_signal	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	SO	400828	SO:0001527	SO:0000839	peptide_localization_signal	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	SO	400829	SO:0001528	SO:0001527	nuclear_localization_signal	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	SO	400830	SO:0001529	SO:0001527	endosomal_localization_signal	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	SO	400831	SO:0001530	SO:0001527	lysosomal_localization_signal	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	SO	400832	SO:0001531	SO:0001527	nuclear_export_signal	SO:0000839
2	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A region recognized by a recombinase." [SO:ke]	SO	400833	SO:0001532	SO:0000299	recombination_signal_sequence	SO:0000669
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	400834	SO:0001533	SO:0000162	cryptic_splice_site	SO:0000835
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	SO	400835	SO:0001534	SO:0001527	nuclear_rim_localization_signal	SO:0000839
2	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	400836	SO:0001535	SO:0000182	p_element	SO:0000101
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	SO	400837	SO:0001538	SO:0001536	transcript_function_variant	SO:0001060
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	SO	400838	SO:0001539	SO:0001536	translational_product_function_variant	SO:0001060
2	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant which alters the level of a transcript." [SO:ke]	SO	400839	SO:0001540	SO:0001538	level_of_transcript_variant	SO:0001536
2	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	400840	SO:0001541	SO:0001540	decreased_transcript_level_variant	SO:0001538
2	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	400841	SO:0001542	SO:0001540	increased_transcript_level_variant	SO:0001538
2	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	SO	400842	SO:0001543	SO:0001538	transcript_processing_variant	SO:0001536
2	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]	SO	400843	SO:0001544	SO:0001543	editing_variant	SO:0001538
2	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]	SO	400844	SO:0001545	SO:0001543	polyadenylation_variant	SO:0001538
2	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]	SO	400845	SO:0001546	SO:0001538	transcript_stability_variant	SO:0001536
2	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]	SO	400846	SO:0001547	SO:0001546	decreased_transcript_stability_variant	SO:0001538
2	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]	SO	400847	SO:0001548	SO:0001546	increased_transcript_stability_variant	SO:0001538
2	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]	SO	400848	SO:0001549	SO:0001538	transcription_variant	SO:0001536
2	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]	SO	400849	SO:0001550	SO:0001549	rate_of_transcription_variant	SO:0001538
2	"A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]	\N	transcription_variant	\N	\N	sequence	"A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	400850	SO:0001551	SO:0001550	increased_transcription_rate_variant	SO:0001549
2	"A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]	\N	transcription_variant	\N	\N	sequence	"A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	400851	SO:0001552	SO:0001550	decreased_transcription_rate_variant	SO:0001549
2	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]	SO	400852	SO:0001553	SO:0001539	translational_product_level_variant	SO:0001536
2	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	SO	400853	SO:0001554	SO:0001539	polypeptide_function_variant	SO:0001536
2	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]	SO	400854	SO:0001555	SO:0001553	decreased_translational_product_level	SO:0001539
2	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]	SO	400855	SO:0001556	SO:0001553	increased_translational_product_level	SO:0001539
2	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]	SO	400856	SO:0001557	SO:0001554	polypeptide_gain_of_function_variant	SO:0001539
2	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]	SO	400857	SO:0001558	SO:0001554	polypeptide_localization_variant	SO:0001539
2	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	SO	400858	SO:0001559	SO:0001554	polypeptide_loss_of_function_variant	SO:0001539
2	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	\N	polypeptide_function_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]	SO	400859	SO:0001560	SO:0001559	inactive_ligand_binding_site	SO:0001554
2	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	\N	polypeptide_function_variant	\N	\N	sequence	"A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]	SO	400860	SO:0001561	SO:0001559	polypeptide_partial_loss_of_function	SO:0001554
2	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]	SO	400861	SO:0001562	SO:0001554	polypeptide_post_translational_processing_variant	SO:0001539
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]	SO	400862	SO:0001563	SO:0001537	copy_number_change	SO:0001060
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where the structure of the gene is changed." [SO:ke]	SO	400863	SO:0001564	SO:0001878	gene_variant	SO:0001537
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby a two genes have become joined." [SO:ke]	SO	400864	SO:0001565	SO:0001564	gene_fusion	SO:0001878
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located within a regulatory region." [SO:ke]	SO	400865	SO:0001566	SO:0001878	regulatory_region_variant	SO:0001537
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	400866	SO:0001567	SO:0001590	stop_retained_variant	SO:0001580
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	400867	SO:0001567	SO:0001819	stop_retained_variant	SO:0001580
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that changes the process of splicing." [SO:ke]	SO	400868	SO:0001568	SO:0001576	splicing_variant	SO:0001564
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	400869	SO:0001569	SO:0001568	cryptic_splice_site_variant	SO:0001576
2	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	SO	400870	SO:0001570	SO:0001569	cryptic_splice_acceptor	SO:0001568
2	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	SO	400871	SO:0001571	SO:0001569	cryptic_splice_donor	SO:0001568
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby an exon is lost from the transcript." [SO:ke]	SO	400872	SO:0001572	SO:0001568	exon_loss_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	400873	SO:0001573	SO:0001568	intron_gain	SO:0001576
2	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	400874	SO:0001574	SO:0001629	splice_acceptor_variant	SO:0001568
2	"A transcript variant occurring within an intron." [SO:ke]	\N	intron_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	400875	SO:0001574	SO:0001629	splice_acceptor_variant	SO:0001627
2	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	400876	SO:0001575	SO:0001629	splice_donor_variant	SO:0001568
2	"A transcript variant occurring within an intron." [SO:ke]	\N	intron_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	400877	SO:0001575	SO:0001629	splice_donor_variant	SO:0001627
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that changes the structure of the transcript." [SO:ke]	SO	400878	SO:0001576	SO:0001564	transcript_variant	SO:0001878
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]	SO	400879	SO:0001577	SO:0001576	complex_transcript_variant	SO:0001564
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	400880	SO:0001578	SO:0001590	stop_lost	SO:0001580
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	400881	SO:0001578	SO:0001907	stop_lost	SO:0001878
2	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	400882	SO:0001578	SO:0001992	stop_lost	SO:0001650
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	400883	SO:0001580	SO:0001791	coding_sequence_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	400884	SO:0001580	SO:0001968	coding_sequence_variant	SO:0001576
2	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	400885	SO:0001582	SO:0001580	initiator_codon_variant	SO:0001791
2	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	400886	SO:0001582	SO:0001580	initiator_codon_variant	SO:0001968
2	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	400887	SO:0001583	SO:0001992	missense_variant	SO:0001650
2	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	400888	SO:0001585	SO:0001583	conservative_missense_variant	SO:0001992
2	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	400889	SO:0001586	SO:0001583	non_conservative_missense_variant	SO:0001992
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	400890	SO:0001587	SO:0001906	stop_gained	SO:0001878
2	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	400891	SO:0001587	SO:0001992	stop_gained	SO:0001650
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	400892	SO:0001589	SO:0001818	frameshift_variant	SO:0001580
2	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	400893	SO:0001590	SO:0001580	terminator_codon_variant	SO:0001791
2	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	400894	SO:0001590	SO:0001580	terminator_codon_variant	SO:0001968
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	400895	SO:0001591	SO:0001589	frame_restoring_variant	SO:0001818
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	400896	SO:0001592	SO:0001589	minus_1_frameshift_variant	SO:0001818
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"" []	SO	400897	SO:0001593	SO:0001589	minus_2_frameshift_variant	SO:0001818
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	400898	SO:0001594	SO:0001589	plus_1_frameshift_variant	SO:0001818
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"" []	SO	400899	SO:0001595	SO:0001589	plus_2_frameshift_variant	SO:0001818
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]	SO	400900	SO:0001596	SO:0001576	transcript_secondary_structure_variant	SO:0001564
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]	SO	400901	SO:0001597	SO:0001596	compensatory_transcript_secondary_structure_variant	SO:0001576
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	SO	400902	SO:0001598	SO:0001564	translational_product_structure_variant	SO:0001878
2	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	400903	SO:0001599	SO:0001539	3D_polypeptide_structure_variant	SO:0001536
2	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	400904	SO:0001600	SO:0001599	complex_3D_structural_variant	SO:0001539
2	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]	SO	400905	SO:0001601	SO:0001599	conformational_change_variant	SO:0001539
2	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"" []	SO	400906	SO:0001602	SO:0001539	complex_change_of_translational_product_variant	SO:0001536
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	SO	400907	SO:0001603	SO:0001598	polypeptide_sequence_variant	SO:0001564
2	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]	SO	400908	SO:0001604	SO:0001603	amino_acid_deletion	SO:0001598
2	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]	SO	400909	SO:0001605	SO:0001603	amino_acid_insertion	SO:0001598
2	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	SO	400910	SO:0001606	SO:0001603	amino_acid_substitution	SO:0001598
2	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	SO	400911	SO:0001607	SO:0001606	conservative_amino_acid_substitution	SO:0001603
2	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	SO	400912	SO:0001608	SO:0001606	non_conservative_amino_acid_substitution	SO:0001603
2	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	SO	400913	SO:0001609	SO:0001603	elongated_polypeptide	SO:0001598
2	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	400914	SO:0001610	SO:0001609	elongated_polypeptide_C_terminal	SO:0001603
2	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	400915	SO:0001611	SO:0001609	elongated_polypeptide_N_terminal	SO:0001603
2	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	\N	elongated_polypeptide	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	400916	SO:0001612	SO:0001610	elongated_in_frame_polypeptide_C_terminal	SO:0001609
2	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	\N	elongated_polypeptide	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	400917	SO:0001613	SO:0001610	elongated_out_of_frame_polypeptide_C_terminal	SO:0001609
2	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	\N	elongated_polypeptide	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	400918	SO:0001614	SO:0001611	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001609
2	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	\N	elongated_polypeptide	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	400919	SO:0001615	SO:0001611	elongated_out_of_frame_polypeptide_N_terminal	SO:0001609
2	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]	SO	400920	SO:0001616	SO:0001603	polypeptide_fusion	SO:0001598
2	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]	SO	400921	SO:0001617	SO:0001603	polypeptide_truncation	SO:0001598
2	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	\N	polypeptide_loss_of_function_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]	SO	400922	SO:0001618	SO:0001560	inactive_catalytic_site	SO:0001559
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant of a non coding RNA gene." [SO:ke]	SO	400923	SO:0001619	SO:0001576	non_coding_transcript_variant	SO:0001564
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant located with the sequence of the mature miRNA." [SO:ke]	SO	400924	SO:0001620	SO:0001619	mature_miRNA_variant	SO:0001576
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A variant in a transcript that is the target of NMD." [SO:ke]	SO	400925	SO:0001621	SO:0001576	NMD_transcript_variant	SO:0001564
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	400926	SO:0001622	SO:0001791	UTR_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	400927	SO:0001622	SO:0001968	UTR_variant	SO:0001576
2	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	400928	SO:0001623	SO:0001622	5_prime_UTR_variant	SO:0001791
2	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	400929	SO:0001623	SO:0001622	5_prime_UTR_variant	SO:0001968
2	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	400930	SO:0001624	SO:0001622	3_prime_UTR_variant	SO:0001791
2	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	400931	SO:0001624	SO:0001622	3_prime_UTR_variant	SO:0001968
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	400932	SO:0001626	SO:0001590	incomplete_terminal_codon_variant	SO:0001580
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	400933	SO:0001626	SO:0001650	incomplete_terminal_codon_variant	SO:0001818
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant occurring within an intron." [SO:ke]	SO	400934	SO:0001627	SO:0001576	intron_variant	SO:0001564
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located in the intergenic region, between genes." [SO:ke]	SO	400935	SO:0001628	SO:0001878	intergenic_variant	SO:0001537
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	400936	SO:0001629	SO:0001568	splice_site_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	400937	SO:0001629	SO:0001627	splice_site_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]	SO	400938	SO:0001630	SO:0001568	splice_region_variant	SO:0001576
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located 5' of a gene." [SO:ke]	SO	400939	SO:0001631	SO:0001628	upstream_gene_variant	SO:0001878
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located 3' of a gene." [SO:ke]	SO	400940	SO:0001632	SO:0001628	downstream_gene_variant	SO:0001878
2	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A sequence variant located within 5 KB of the end of a gene." [SO:ke]	SO	400941	SO:0001633	SO:0001632	5KB_downstream_variant	SO:0001628
2	"A sequence variant located 3' of a gene." [SO:ke]	\N	downstream_gene_variant	\N	\N	sequence	"A sequence variant located within a half KB of the end of a gene." [SO:ke]	SO	400942	SO:0001634	SO:0001633	500B_downstream_variant	SO:0001632
2	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A sequence variant located within 5KB 5' of a gene." [SO:ke]	SO	400943	SO:0001635	SO:0001631	5KB_upstream_variant	SO:0001628
2	"A sequence variant located 5' of a gene." [SO:ke]	\N	upstream_gene_variant	\N	\N	sequence	"A sequence variant located within 2KB 5' of a gene." [SO:ke]	SO	400944	SO:0001636	SO:0001635	2KB_upstream_variant	SO:0001631
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes for ribosomal RNA." [SO:ke]	SO	400945	SO:0001637	SO:0001263	rRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes for an piwi associated RNA." [SO:ke]	SO	400946	SO:0001638	SO:0001263	piRNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes an RNase P RNA." [SO:ke]	SO	400947	SO:0001639	SO:0001263	RNase_P_RNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes a RNase_MRP_RNA." [SO:ke]	SO	400948	SO:0001640	SO:0001263	RNase_MRP_RNA_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes large intervening non-coding RNA." [SO:ke]	SO	400949	SO:0001641	SO:0001263	lincRNA_gene	SO:0000704
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill]	SO	400950	SO:0001642	SO:0001410	mathematically_defined_repeat	SO:0000001
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]	SO	400951	SO:0001643	SO:0001263	telomerase_RNA_gene	SO:0000704
2	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	400952	SO:0001644	SO:0000440	targeting_vector	SO:0000151
2	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	400953	SO:0001644	SO:0000440	targeting_vector	SO:0001235
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	400954	SO:0001644	SO:0000804	targeting_vector	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	400955	SO:0001644	SO:0000804	targeting_vector	SO:0001409
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A measurable sequence feature that varies within a population." [SO:db]	SO	400956	SO:0001645	SO:0001411	genetic_marker	SO:0000001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]	SO	400957	SO:0001646	SO:0001645	DArT_marker	SO:0001411
2	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	five_prime_UTR	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	400958	SO:0001647	SO:0000139	kozak_sequence	SO:0000204
2	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	400959	SO:0001647	SO:0000139	kozak_sequence	SO:0000836
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposon that is disrupted by the insertion of another element." [SO:ke]	SO	400960	SO:0001648	SO:0000101	nested_transposon	SO:0001039
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat that is disrupted by the insertion of another element." [SO:ke]	SO	400961	SO:0001649	SO:0000657	nested_repeat	SO:0001411
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	400962	SO:0001650	SO:0001818	inframe_variant	SO:0001580
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	400963	SO:0001653	SO:0000713	retinoic_acid_responsive_element	SO:0000714
2	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	400964	SO:0001653	SO:0000167	retinoic_acid_responsive_element	SO:0001055
2	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SOFA	binding_site	biosapiens,SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	400965	SO:0001654	SO:0000410	nucleotide_to_protein_binding_site	SO:0000409
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	SO	400966	SO:0001655	SO:0000409	nucleotide_binding_site	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	SO	400967	SO:0001656	SO:0000409	metal_binding_site	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]	SO	400968	SO:0001657	SO:0000409	ligand_binding_site	SO:0001411
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]	SO	400969	SO:0001658	SO:0001649	nested_tandem_repeat	SO:0000657
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"" []	SO	400970	SO:0001659	SO:0000713	promoter_element	SO:0000714
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"" []	SO	400971	SO:0001660	SO:0001659	core_promoter_element	SO:0000713
2	"" []	\N	core_promoter_element	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	400972	SO:0001661	SO:0000174	RNA_polymerase_II_TATA_box	SO:0001660
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	400973	SO:0001661	SO:0001669	RNA_polymerase_II_TATA_box	SO:0000170
2	"" []	\N	core_promoter_element	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	400974	SO:0001662	SO:0000174	RNA_polymerase_III_TATA_box	SO:0001660
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	400975	SO:0001662	SO:0000171	RNA_polymerase_III_TATA_box	SO:0001203
2	"" []	\N	promoter_element	\N	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	400976	SO:0001663	SO:0001660	BREd_motif	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	400977	SO:0001663	SO:0001669	BREd_motif	SO:0000170
2	"" []	\N	promoter_element	\N	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	400978	SO:0001664	SO:0001660	DCE	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	400979	SO:0001664	SO:0001669	DCE	SO:0000170
5	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	1641336	SO:0001665	SO:0000713	DCE_SI	SO:0000714
2	"" []	\N	core_promoter_element	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	400981	SO:0001665	SO:0001664	DCE_SI	SO:0001660
2	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	400982	SO:0001665	SO:0001664	DCE_SI	SO:0001669
5	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	1641339	SO:0001666	SO:0000713	DCE_SII	SO:0000714
2	"" []	\N	core_promoter_element	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	400984	SO:0001666	SO:0001664	DCE_SII	SO:0001660
2	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	400985	SO:0001666	SO:0001664	DCE_SII	SO:0001669
5	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	1641342	SO:0001667	SO:0000713	DCE_SIII	SO:0000714
2	"" []	\N	core_promoter_element	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	400987	SO:0001667	SO:0001664	DCE_SIII	SO:0001660
2	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	\N	RNApol_II_core_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	400988	SO:0001667	SO:0001664	DCE_SIII	SO:0001669
2	"" []	\N	promoter_element	\N	\N	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	400989	SO:0001668	SO:0001678	proximal_promoter_element	SO:0001659
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	400990	SO:0001669	SO:0000170	RNApol_II_core_promoter	SO:0001203
2	"" []	\N	promoter_element	\N	\N	sequence	"" []	SO	400991	SO:0001670	SO:0001678	distal_promoter_element	SO:0001659
2	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"" []	SO	400992	SO:0001671	SO:0000613	bacterial_RNApol_promoter_sigma_70	SO:0000752
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"" []	SO	400993	SO:0001671	SO:0000613	bacterial_RNApol_promoter_sigma_70	SO:0001203
2	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"" []	SO	400994	SO:0001672	SO:0000613	bacterial_RNApol_promoter_sigma54	SO:0000752
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"" []	SO	400995	SO:0001672	SO:0000613	bacterial_RNApol_promoter_sigma54	SO:0001203
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	400996	SO:0001673	SO:0000713	minus_12_signal	SO:0000714
2	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	400997	SO:0001673	SO:0001672	minus_12_signal	SO:0000613
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	400998	SO:0001674	SO:0000713	minus_24_signal	SO:0000714
2	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	\N	bacterial_RNApol_promoter	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	400999	SO:0001674	SO:0001672	minus_24_signal	SO:0000613
2	"" []	\N	core_promoter_element	\N	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	401000	SO:0001675	SO:0000619	A_box_type_1	SO:0001660
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	401001	SO:0001675	SO:0000617	A_box_type_1	SO:0000171
2	"" []	\N	core_promoter_element	\N	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	401002	SO:0001676	SO:0000619	A_box_type_2	SO:0001660
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	401003	SO:0001676	SO:0000618	A_box_type_2	SO:0000171
2	"" []	\N	promoter_element	\N	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	401004	SO:0001677	SO:0001660	intermediate_element	SO:0001659
2	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	\N	RNApol_III_promoter	\N	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	401005	SO:0001677	SO:0000617	intermediate_element	SO:0000171
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	SO	401006	SO:0001678	SO:0001659	regulatory_promoter_element	SO:0000713
2	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SO	401007	SO:0001679	SO:0005836	transcription_regulatory_region	SO:0000831
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of translation." [SO:ke]	SO	401008	SO:0001680	SO:0005836	translation_regulatory_region	SO:0000831
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of recombination." [SO:ke]	SO	401009	SO:0001681	SO:0005836	recombination_regulatory_region	SO:0000831
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]	SO	401010	SO:0001682	SO:0005836	replication_regulatory_region	SO:0000831
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	SO	401011	SO:0001683	SO:0001411	sequence_motif	SO:0000001
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute of an experimentally derived feature." [SO:ke]	SO	401012	SO:0001684	SO:0000733	experimental_feature_attribute	SO:0000400
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The score of an experimentally derived feature such as a p-value." [SO:ke]	SO	401013	SO:0001685	SO:0001684	score	SO:0000733
2	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]	SO	401014	SO:0001686	SO:0001684	quality_value	SO:0000733
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	SO	401015	SO:0001687	SO:0001954	restriction_enzyme_recognition_site	SO:0001411
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]	SO	401016	SO:0001688	SO:0000699	restriction_enzyme_cleavage_junction	SO:0000110
2	"The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]	\N	restriction_enzyme_cleavage_junction	\N	\N	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	401017	SO:0001689	SO:0001694	five_prime_restriction_enzyme_junction	SO:0001688
2	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	401018	SO:0001689	SO:0001692	five_prime_restriction_enzyme_junction	SO:0001687
2	"The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]	\N	restriction_enzyme_cleavage_junction	\N	\N	sequence	"" []	SO	401019	SO:0001690	SO:0001694	three_prime_restriction_enzyme_junction	SO:0001688
2	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"" []	SO	401020	SO:0001690	SO:0001692	three_prime_restriction_enzyme_junction	SO:0001687
2	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"" []	SO	401021	SO:0001691	SO:0001687	blunt_end_restriction_enzyme_cleavage_site	SO:0001954
2	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"" []	SO	401022	SO:0001692	SO:0001687	sticky_end_restriction_enzyme_cleavage_site	SO:0001954
2	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	401023	SO:0001693	SO:0001688	blunt_end_restriction_enzyme_cleavage_junction	SO:0000699
2	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	401024	SO:0001693	SO:0001691	blunt_end_restriction_enzyme_cleavage_junction	SO:0001687
2	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]	SO	401025	SO:0001694	SO:0001688	single_strand_restriction_enzyme_cleavage_site	SO:0000699
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	SO	1166812	SO:0001695	SO:0001954	restriction_enzyme_single_strand_overhang	SO:0001411
2	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	SO	401027	SO:0001695	SO:0001692	restriction_enzyme_single_strand_overhang	SO:0001687
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]	SO	401028	SO:0001696	SO:0001410	experimentally_defined_binding_region	SO:0000001
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]	SO	401029	SO:0001697	SO:0001696	ChIP_seq_region	SO:0001410
2	"A single stranded oligonucleotide." [SO:ke]	\N	ss_oligo	SOFA	SOFA	sequence	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	SO	401030	SO:0001698	SO:0000112	ASPE_primer	SO:0000441
2	"A single stranded oligonucleotide." [SO:ke]	\N	ss_oligo	SOFA	SOFA	sequence	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	SO	401031	SO:0001699	SO:0000112	dCAPS_primer	SO:0000441
2	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	401032	SO:0001700	SO:0001089	histone_modification	SO:0100001
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	401033	SO:0001700	SO:0001720	histone_modification	SO:0001411
2	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	401034	SO:0001701	SO:0001700	histone_methylation_site	SO:0001089
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	401035	SO:0001701	SO:0001700	histone_methylation_site	SO:0001720
2	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	401036	SO:0001702	SO:0001700	histone_acetylation_site	SO:0001089
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	401037	SO:0001702	SO:0001700	histone_acetylation_site	SO:0001720
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	401038	SO:0001703	SO:0001973	H3K9_acetylation_site	SO:0001702
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	401039	SO:0001704	SO:0001973	H3K14_acetylation_site	SO:0001702
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401040	SO:0001705	SO:0001734	H3K4_monomethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401041	SO:0001706	SO:0001734	H3K4_trimethylation	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401042	SO:0001707	SO:0001736	H3K9_trimethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401043	SO:0001708	SO:0001732	H3K27_monomethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401044	SO:0001709	SO:0001732	H3K27_trimethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401045	SO:0001710	SO:0001735	H3K79_monomethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401046	SO:0001711	SO:0001735	H3K79_dimethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401047	SO:0001712	SO:0001735	H3K79_trimethylation_site	SO:0001701
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401048	SO:0001713	SO:0001701	H4K20_monomethylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	401049	SO:0001714	SO:0001701	H2BK5_monomethylation_site	SO:0001700
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	SO	401050	SO:0001715	SO:0001055	ISRE	SO:0001679
2	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	401051	SO:0001716	SO:0001700	histone_ubiqitination_site	SO:0001089
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	401052	SO:0001716	SO:0001700	histone_ubiqitination_site	SO:0001720
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	401053	SO:0001717	SO:0001716	H2B_ubiquitination_site	SO:0001700
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	401054	SO:0001718	SO:0001973	H3K18_acetylation_site	SO:0001702
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	401055	SO:0001719	SO:0001973	H3K23_acylation_site	SO:0001702
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SO	401056	SO:0001720	SO:0001411	epigenetically_modified_region	SO:0000001
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	401057	SO:0001721	SO:0001973	H3K27_acylation_site	SO:0001702
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	401058	SO:0001722	SO:0001733	H3K36_monomethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	401059	SO:0001723	SO:0001733	H3K36_dimethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	401060	SO:0001724	SO:0001733	H3K36_trimethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	401061	SO:0001725	SO:0001734	H3K4_dimethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	401062	SO:0001726	SO:0001732	H3K27_dimethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	401063	SO:0001727	SO:0001736	H3K9_monomethylation_site	SO:0001701
2	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	\N	histone_methylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	401064	SO:0001728	SO:0001736	H3K9_dimethylation_site	SO:0001701
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	401065	SO:0001729	SO:0001972	H4K16_acylation_site	SO:0001702
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	401066	SO:0001730	SO:0001972	H4K5_acylation_site	SO:0001702
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	401067	SO:0001731	SO:0001972	H4K8_acylation_site	SO:0001702
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	401068	SO:0001732	SO:0001701	H3K27_methylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	401069	SO:0001733	SO:0001701	H3K36_methylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	401070	SO:0001734	SO:0001701	H3K4_methylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	401071	SO:0001735	SO:0001701	H3K79_methylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	401072	SO:0001736	SO:0001701	H3K9_methylation_site	SO:0001700
2	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	401073	SO:0001737	SO:0001700	histone_acylation_region	SO:0001089
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	401074	SO:0001737	SO:0001700	histone_acylation_region	SO:0001720
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	401075	SO:0001738	SO:0001737	H4K_acylation_region	SO:0001700
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene with a start codon other than AUG." [SO:xp]	SO	401076	SO:0001739	SO:0000704	gene_with_non_canonical_start_codon	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene with a translational start codon of CUG." [SO:mc]	SO	401077	SO:0001740	SO:0001739	gene_with_start_codon_CUG	SO:0000704
2	"" []	\N	gene_component_region	SOFA	\N	sequence	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	SO	401078	SO:0001741	SO:3000000	pseudogenic_gene_segment	SO:0000842
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR	sequence_alteration	SOFA	SOFA	sequence	"A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]	SO	401079	SO:0001742	SO:0001019	copy_number_gain	SO:0001059
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR	sequence_alteration	SOFA	SOFA	sequence	"A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]	SO	401080	SO:0001743	SO:0001019	copy_number_loss	SO:0001059
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR	sequence_feature	SOFA	SOFA	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]	SO	401081	SO:0001744	SO:0001059	UPD	SO:0000110
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm]	SO	401082	SO:0001745	SO:0001744	maternal_uniparental_disomy	SO:0001059
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm]	SO	401083	SO:0001746	SO:0001744	paternal_uniparental_disomy	SO:0001059
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb]	SO	401084	SO:0001747	SO:0001411	open_chromatin_region	SO:0000001
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401085	SO:0001748	SO:0000709	SL3_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401086	SO:0001749	SO:0000709	SL4_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401087	SO:0001750	SO:0000709	SL5_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401088	SO:0001751	SO:0000709	SL6_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401089	SO:0001752	SO:0000709	SL7_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401090	SO:0001753	SO:0000709	SL8_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401091	SO:0001754	SO:0000709	SL9_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401092	SO:0001755	SO:0000709	SL10_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401093	SO:0001756	SO:0000709	SL11_acceptor_site	SO:0000706
2	"The 3' splice site of the acceptor primary transcript." [SO:ke]	\N	trans_splice_acceptor_site	SOFA	\N	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	401094	SO:0001757	SO:0000709	SL12_acceptor_site	SO:0000706
2	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]	SO	401095	SO:0001758	SO:0001760	duplicated_pseudogene	SO:0000336
2	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	\N	pseudogene	SOFA	\N	sequence	"A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]	SO	401096	SO:0001759	SO:0001760	unitary_pseudogene	SO:0000336
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	SO	401097	SO:0001760	SO:0000336	non_processed_pseudogene	SO:0001411
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]	SO	401098	SO:0001762	SO:0001761	variant_origin	SO:0000400
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]	SO	401099	SO:0001763	SO:0001761	variant_frequency	SO:0000400
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]	SO	401100	SO:0001764	SO:0001763	unique_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401101	SO:0001765	SO:0001763	rare_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401102	SO:0001766	SO:0001763	polymorphic_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401103	SO:0001767	SO:0001763	common_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401104	SO:0001768	SO:0001763	fixed_variant	SO:0001761
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]	SO	401105	SO:0001769	SO:0001761	variant_phenotype	SO:0000400
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401106	SO:0001770	SO:0001769	benign_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401107	SO:0001771	SO:0001769	disease_associated_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401108	SO:0001772	SO:0001769	disease_causing_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401109	SO:0001773	SO:0001769	lethal_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401110	SO:0001774	SO:0001769	quantitative_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401111	SO:0001775	SO:0001762	maternal_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401112	SO:0001776	SO:0001762	paternal_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401113	SO:0001777	SO:0001762	somatic_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401114	SO:0001778	SO:0001762	germline_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401115	SO:0001779	SO:0001762	pedigree_specific_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401116	SO:0001780	SO:0001762	population_specific_variant	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401117	SO:0001781	SO:0001762	de_novo_variant	SO:0001761
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located within a transcription factor binding site." [EBI:fc]	SO	401118	SO:0001782	SO:0001566	TF_binding_site_variant	SO:0001878
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR	sequence_alteration	SOFA	DBVAR	sequence	"A structural sequence alteration or rearrangement encompassing one or more genome fragments." [NCBI:th, SO:ke]	SO	401119	SO:0001784	SO:0001785	complex_structural_alteration	SO:0001059
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR	sequence_feature	SOFA	SOFA	sequence	"" []	SO	401120	SO:0001785	SO:0001059	structural_alteration	SO:0000110
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	DBVAR	sequence_variant	\N	\N	sequence	"A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke]	SO	401121	SO:0001786	SO:0001536	loss_of_heterozygosity	SO:0001060
2	"A sequence variant that changes the process of splicing." [SO:ke]	\N	splicing_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	401122	SO:0001787	SO:0001629	splice_donor_5th_base_variant	SO:0001568
2	"A transcript variant occurring within an intron." [SO:ke]	\N	intron_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	401123	SO:0001787	SO:0001629	splice_donor_5th_base_variant	SO:0001627
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	401124	SO:0001788	SO:0000330	U_box	SO:0001410
2	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	401125	SO:0001788	SO:0000186	U_box	SO:0000180
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	SO	401126	SO:0001789	SO:0005855	mating_type_region	SO:0001411
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]	SO	401127	SO:0001790	SO:0000143	paired_end_fragment	SO:0001410
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that changes exon sequence." [SO:ke]	SO	401128	SO:0001791	SO:0001576	exon_variant	SO:0001564
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	401129	SO:0001792	SO:0001619	non_coding_transcript_exon_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	401130	SO:0001792	SO:0001791	non_coding_transcript_exon_variant	SO:0001576
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	401131	SO:0001793	SO:0000150	clone_end	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	401132	SO:0001793	SO:0000150	clone_end	SO:0000149
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	401133	SO:0001793	SO:0000151	clone_end	SO:0000695
2	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	401134	SO:0001794	SO:0000577	point_centromere	SO:0000628
2	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	401135	SO:0001795	SO:0000577	regional_centromere	SO:0000628
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	401136	SO:0001796	SO:0000330	regional_centromere_central_core	SO:0001410
2	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	401137	SO:0001796	SO:0001795	regional_centromere_central_core	SO:0000577
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat region found within the modular centromere." [SO:ke]	SO	401138	SO:0001797	SO:0000657	centromeric_repeat	SO:0001411
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	401139	SO:0001798	SO:0001797	regional_centromere_inner_repeat_region	SO:0000657
2	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	\N	conserved_region	SOFA	\N	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	401140	SO:0001798	SO:0001796	regional_centromere_inner_repeat_region	SO:0000330
2	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	\N	regional_centromere	\N	\N	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	401141	SO:0001798	SO:0001796	regional_centromere_inner_repeat_region	SO:0001795
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	401142	SO:0001799	SO:0001797	regional_centromere_outer_repeat_region	SO:0000657
2	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	401143	SO:0001799	SO:0001795	regional_centromere_outer_repeat_region	SO:0000577
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	SO	401144	SO:0001800	SO:0000655	tasiRNA	SO:0000233
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a tasiRNA." [PMID:16145017]	SO	401145	SO:0001801	SO:0000483	tasiRNA_primary_transcript	SO:0000185
2	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_processing_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]	SO	401146	SO:0001802	SO:0001545	increased_polyadenylation_variant	SO:0001543
2	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_processing_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]	SO	401147	SO:0001803	SO:0001545	decreased_polyadenylation_variant	SO:0001543
2	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	biosapiens	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	401148	SO:0001804	SO:0001093	DDB_box	SO:0000410
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	\N	molecular_contact_region	biosapiens	biosapiens	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	401149	SO:0001804	SO:0001093	DDB_box	SO:0100002
2	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	401150	SO:0001805	SO:0100017	destruction_box	SO:0001067
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	SO	401151	SO:0001806	SO:0001527	ER_retention_signal	SO:0000839
2	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	401152	SO:0001807	SO:0100017	KEN_box	SO:0001067
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	SO	401153	SO:0001808	SO:0001527	mitochondrial_targeting_signal	SO:0000839
2	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	\N	propeptide	biosapiens	biosapiens,SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	401154	SO:0001809	SO:0000418	signal_anchor	SO:0001062
2	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	\N	peptide_localization_signal	SOFA	biosapiens,SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	401155	SO:0001809	SO:0000418	signal_anchor	SO:0001527
2	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	biosapiens	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	401156	SO:0001810	SO:0001093	PIP_box	SO:0000410
2	"A region that is involved a contact with another molecule." [EBIBS:GAR]	\N	molecular_contact_region	biosapiens	biosapiens	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	401157	SO:0001810	SO:0001093	PIP_box	SO:0100002
2	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	401158	SO:0001811	SO:0001089	phosphorylation_site	SO:0100001
2	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	\N	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	401159	SO:0001812	SO:0001114	transmembrane_helix	SO:0001078
2	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	\N	intramembrane_polypeptide_region	biosapiens	biosapiens	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	401160	SO:0001812	SO:0001077	transmembrane_helix	SO:0001075
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	SO	401161	SO:0001813	SO:0001527	vacuolar_sorting_signal	SO:0000839
2	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	401162	SO:0001814	SO:0001761	coding_variant_quality	SO:0000400
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401163	SO:0001815	SO:0001814	synonymous	SO:0001761
2	"A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]	\N	variant_quality	\N	\N	sequence	"" []	SO	401164	SO:0001816	SO:0001814	non_synonymous	SO:0001761
2	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]	SO	401165	SO:0001817	SO:0000863	inframe	SO:0000237
2	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	401166	SO:0001818	SO:0001580	protein_altering_variant	SO:0001791
2	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	401167	SO:0001818	SO:0001580	protein_altering_variant	SO:0001968
2	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	401168	SO:0001819	SO:0001580	synonymous_variant	SO:0001791
2	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	401169	SO:0001819	SO:0001580	synonymous_variant	SO:0001968
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	401170	SO:0001820	SO:0001650	inframe_indel	SO:0001818
2	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	401171	SO:0001821	SO:0001820	inframe_insertion	SO:0001650
2	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_elongation	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	401172	SO:0001821	SO:0001908	inframe_insertion	SO:0001907
2	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	401173	SO:0001822	SO:0001820	inframe_deletion	SO:0001650
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	401174	SO:0001822	SO:0001906	inframe_deletion	SO:0001878
2	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	\N	inframe_indel	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	401175	SO:0001823	SO:0001821	conservative_inframe_insertion	SO:0001820
2	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	\N	internal_feature_elongation	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	401176	SO:0001823	SO:0001821	conservative_inframe_insertion	SO:0001908
2	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	\N	inframe_indel	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	401177	SO:0001824	SO:0001821	disruptive_inframe_insertion	SO:0001820
2	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	\N	internal_feature_elongation	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	401178	SO:0001824	SO:0001821	disruptive_inframe_insertion	SO:0001908
2	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	\N	inframe_indel	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	401179	SO:0001825	SO:0001822	conservative_inframe_deletion	SO:0001820
2	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_truncation	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	401180	SO:0001825	SO:0001822	conservative_inframe_deletion	SO:0001906
2	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	\N	inframe_indel	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	401181	SO:0001826	SO:0001822	disruptive_inframe_deletion	SO:0001820
2	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_truncation	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	401182	SO:0001826	SO:0001822	disruptive_inframe_deletion	SO:0001906
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	401183	SO:0001827	SO:0000150	mRNA_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	401184	SO:0001827	SO:0000150	mRNA_read	SO:0000149
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	401185	SO:0001828	SO:0000150	genomic_DNA_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	401186	SO:0001828	SO:0000150	genomic_DNA_read	SO:0000149
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	401187	SO:0001829	SO:0000149	mRNA_contig	SO:0000143
2	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	401188	SO:0001829	SO:0000149	mRNA_contig	SO:0000148
2	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	401189	SO:0001829	SO:0000149	mRNA_contig	SO:0000353
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]	SO	401190	SO:0001830	SO:0000006	AFLP_fragment	SO:0000695
2	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	\N	match	SOFA	SOFA	sequence	"A match to a protein HMM such as pfam." [SO:ke]	SO	401191	SO:0001831	SO:0000349	protein_hmm_match	SO:0000343
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	SO	401192	SO:0001832	SO:0000839	immunoglobulin_region	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	SO	401193	SO:0001832	SO:0000839	immunoglobulin_region	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	\N	sequence	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	401194	SO:0001833	SO:0001832	V_region	SO:0000839
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	\N	sequence	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	401195	SO:0001834	SO:0001832	C_region	SO:0000839
2	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	401196	SO:0001835	SO:0000301	N_region	SO:0000300
2	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	401197	SO:0001836	SO:0000301	S_region	SO:0000300
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]	SO	401198	SO:0001837	SO:0000667	mobile_element_insertion	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	DBVAR,SOFA	sequence	"A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]	SO	401199	SO:0001837	SO:0000667	mobile_element_insertion	SO:0001411
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]	SO	401200	SO:0001838	SO:0000667	novel_sequence_insertion	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	DBVAR,SOFA	sequence	"An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]	SO	401201	SO:0001838	SO:0000667	novel_sequence_insertion	SO:0001411
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	SO	401202	SO:0001839	SO:0001659	CSL_response_element	SO:0000713
2	"" []	\N	promoter_element	\N	\N	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	401203	SO:0001840	SO:0001660	GATA_box	SO:0001659
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]	SO	401204	SO:0001841	SO:0000336	polymorphic_pseudogene	SO:0001411
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	SO	401205	SO:0001842	SO:0001659	AP_1_binding_site	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	SO	401206	SO:0001843	SO:0001659	CRE	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	SO	401207	SO:0001844	SO:0001659	CuRE	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	SO	401208	SO:0001845	SO:0001659	DRE	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	SO	401209	SO:0001846	SO:0001659	FLEX_element	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	SO	401210	SO:0001847	SO:0001659	forkhead_motif	SO:0000713
2	"" []	\N	promoter_element	\N	\N	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	401211	SO:0001848	SO:0001660	homol_D_box	SO:0001659
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	SO	401212	SO:0001849	SO:0001659	homol_E_box	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	SO	401213	SO:0001850	SO:0001659	HSE	SO:0000713
2	"" []	\N	core_promoter_element	\N	\N	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	401214	SO:0001851	SO:0001840	iron_repressed_GATA_element	SO:0001660
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	SO	401215	SO:0001852	SO:0001659	mating_type_M_box	SO:0000713
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]	SO	401216	SO:0001853	SO:0000713	androgen_response_element	SO:0000714
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]	SO	401217	SO:0001854	SO:0000051	smFISH_probe	SO:0000696
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	SO	401218	SO:0001855	SO:0001659	MCB	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	SO	401219	SO:0001856	SO:0001659	CCAAT_motif	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	SO	401220	SO:0001857	SO:0001659	Ace2_UAS	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	SO	401221	SO:0001858	SO:0001659	TR_box	SO:0000713
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	SO	401222	SO:0001859	SO:0001659	STREP_motif	SO:0000713
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]	SO	401223	SO:0001860	SO:0000713	rDNA_intergenic_spacer_element	SO:0000714
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	SO	401224	SO:0001861	SO:0001659	sterol_regulatory_element	SO:0000713
2	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	\N	microsatellite	SOFA	\N	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	401225	SO:0001862	SO:0000290	GT_dinucleotide_repeat	SO:0000289
2	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	\N	microsatellite	SOFA	\N	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	401226	SO:0001863	SO:0000291	GTT_trinucleotide_repeat	SO:0000289
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]	SO	401227	SO:0001864	SO:0000713	Sap1_recognition_motif	SO:0000714
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	SO	401228	SO:0001865	SO:0001659	CDRE_motif	SO:0000713
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	401229	SO:0001866	SO:0000149	BAC_read_contig	SO:0000143
2	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	401230	SO:0001866	SO:0000149	BAC_read_contig	SO:0000148
2	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	401231	SO:0001866	SO:0000149	BAC_read_contig	SO:0000353
2	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	\N	vector_replicon	\N	\N	sequence	"A contig of BAC reads." [GMOD:ea]	SO	401232	SO:0001866	SO:0000153	BAC_read_contig	SO:0000440
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene suspected of being involved in the expression of a trait." [GMOD:ea]	SO	401233	SO:0001867	SO:0000704	candidate_gene	SO:0001411
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]	SO	401234	SO:0001868	SO:0001867	positional_candidate_gene	SO:0000704
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]	SO	401235	SO:0001869	SO:0001867	functional_candidate_gene	SO:0000704
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	SO	401236	SO:0001870	SO:0000655	enhancerRNA	SO:0000233
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	SO	401237	SO:0001871	SO:0001659	PCB	SO:0000713
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	SO	401238	SO:0001872	SO:0001411	rearrangement_breakpoint	SO:0000001
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR	sequence	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	SO	401239	SO:0001872	SO:0001785	rearrangement_breakpoint	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	SO	401240	SO:0001873	SO:0001872	interchromosomal_breakpoint	SO:0001411
2	"" []	\N	structural_alteration	DBVAR	\N	sequence	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	SO	401241	SO:0001873	SO:0001872	interchromosomal_breakpoint	SO:0001785
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	SO	401242	SO:0001874	SO:0001872	intrachromosomal_breakpoint	SO:0001411
2	"" []	\N	structural_alteration	DBVAR	\N	sequence	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	SO	401243	SO:0001874	SO:0001872	intrachromosomal_breakpoint	SO:0001785
2	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	401244	SO:0001875	SO:0000148	unassigned_supercontig	SO:0000719
2	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	401245	SO:0001875	SO:0000148	unassigned_supercontig	SO:0001876
2	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SO	401246	SO:0001876	SO:0000353	partial_genomic_sequence_assembly	SO:0001248
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	SO	401247	SO:0001877	SO:0000655	lnc_RNA	SO:0000233
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	SO	401248	SO:0001878	SO:0001537	feature_variant	SO:0001060
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]	SO	401249	SO:0001879	SO:0001537	feature_ablation	SO:0001060
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]	SO	401250	SO:0001880	SO:0001537	feature_amplification	SO:0001060
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]	SO	401251	SO:0001881	SO:0001537	feature_translocation	SO:0001060
2	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]	SO	401252	SO:0001882	SO:0001537	feature_fusion	SO:0001060
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature translocation where the region contains a transcript." [SO:ke]	SO	401253	SO:0001883	SO:0001881	transcript_translocation	SO:0001537
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature translocation where the region contains a regulatory region." [SO:ke]	SO	401254	SO:0001884	SO:0001881	regulatory_region_translocation	SO:0001537
2	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_translocation	\N	\N	sequence	"A feature translocation where the region contains a transcription factor binding site." [SO:ke]	SO	401255	SO:0001885	SO:0001884	TFBS_translocation	SO:0001881
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature fusion where the deletion brings together transcript regions." [SO:ke]	SO	401256	SO:0001886	SO:0001882	transcript_fusion	SO:0001537
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature fusion where the deletion brings together regulatory regions." [SO:ke]	SO	401257	SO:0001887	SO:0001882	regulatory_region_fusion	SO:0001537
2	"A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]	\N	feature_fusion	\N	\N	sequence	"A fusion where the deletion brings together transcription factor binding sites." [SO:ke]	SO	401258	SO:0001888	SO:0001887	TFBS_fusion	SO:0001882
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature amplification of a region containing a transcript." [SO:ke]	SO	401259	SO:0001889	SO:0001880	transcript_amplification	SO:0001537
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]	SO	401260	SO:0001890	SO:0001882	transcript_regulatory_region_fusion	SO:0001537
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature amplification of a region containing a regulatory region." [SO:ke]	SO	401261	SO:0001891	SO:0001880	regulatory_region_amplification	SO:0001537
2	"A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_amplification	\N	\N	sequence	"A feature amplification of a region containing a transcription factor binding site." [SO:ke]	SO	401262	SO:0001892	SO:0001891	TFBS_amplification	SO:0001880
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]	SO	401263	SO:0001893	SO:0001879	transcript_ablation	SO:0001537
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]	SO	401264	SO:0001894	SO:0001879	regulatory_region_ablation	SO:0001537
2	"A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]	\N	feature_ablation	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]	SO	401265	SO:0001895	SO:0001894	TFBS_ablation	SO:0001879
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	401266	SO:0001896	SO:0000316	transposable_element_CDS	SO:0000836
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	401267	SO:0001896	SO:0000101	transposable_element_CDS	SO:0001039
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	401268	SO:0001897	SO:0000336	transposable_element_pseudogene	SO:0001411
2	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	401269	SO:0001897	SO:0000101	transposable_element_pseudogene	SO:0001039
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	734223	SO:0001898	SO:0001797	dg_repeat	SO:0000657
2	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	\N	regional_centromere	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	401271	SO:0001898	SO:0001799	dg_repeat	SO:0001795
2	"A repeat region found within the modular centromere." [SO:ke]	\N	centromeric_repeat	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	401272	SO:0001898	SO:0001799	dg_repeat	SO:0001797
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	734226	SO:0001899	SO:0001797	dh_repeat	SO:0000657
2	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	\N	regional_centromere	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	401274	SO:0001899	SO:0001799	dh_repeat	SO:0001795
2	"A repeat region found within the modular centromere." [SO:ke]	\N	centromeric_repeat	\N	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	401275	SO:0001899	SO:0001799	dh_repeat	SO:0001797
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]	SO	401276	SO:0001900	SO:0000713	M26_binding_site	SO:0000714
2	"" []	\N	promoter_element	\N	\N	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	401277	SO:0001901	SO:0001660	AACCCT_box	SO:0001659
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	401278	SO:0001902	SO:0000835	splice_region	SO:0000185
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	401279	SO:0001902	SO:0000835	splice_region	SO:0000833
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	734229	SO:0001902	SO:0000185	splice_region	SO:0000673
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	401281	SO:0001903	SO:0001877	intronic_lncRNA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	401282	SO:0001904	SO:0001877	antisense_lncRNA	SO:0000655
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]	SO	401283	SO:0001905	SO:0000185	regional_centromere_outer_repeat_transcript	SO:0000673
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	SO	401284	SO:0001906	SO:0001878	feature_truncation	SO:0001537
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	SO	401285	SO:0001907	SO:0001878	feature_elongation	SO:0001537
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	SO	401286	SO:0001908	SO:0001907	internal_feature_elongation	SO:0001878
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	401287	SO:0001909	SO:0001589	frameshift_elongation	SO:0001818
2	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_elongation	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	401288	SO:0001909	SO:0001908	frameshift_elongation	SO:0001907
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	401289	SO:0001910	SO:0001589	frameshift_truncation	SO:0001818
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	401290	SO:0001910	SO:0001906	frameshift_truncation	SO:0001878
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]	SO	401291	SO:0001911	SO:0001563	copy_number_increase	SO:0001537
2	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]	SO	401292	SO:0001912	SO:0001563	copy_number_decrease	SO:0001537
2	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	401293	SO:0001913	SO:0000613	bacterial_RNApol_promoter_sigma_ecf	SO:0000752
2	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	401294	SO:0001913	SO:0000613	bacterial_RNApol_promoter_sigma_ecf	SO:0001203
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]	SO	401295	SO:0001914	SO:0000713	rDNA_replication_fork_barrier	SO:0000714
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]	SO	401296	SO:0001915	SO:0001410	transcription_start_cluster	SO:0000001
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]	SO	401297	SO:0001916	SO:0000324	CAGE_tag	SO:0000696
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]	SO	401298	SO:0001917	SO:0001915	CAGE_cluster	SO:0001410
2	"A nucleotide modified by methylation." [SO:ke]	\N	methylated_DNA_base_feature	SOFA	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	401299	SO:0001918	SO:0000114	5_methylcytosine	SO:0000306
2	"A modified cytosine DNA base feature." [SO:ke]	\N	modified_cytosine	\N	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	401300	SO:0001918	SO:0000114	5_methylcytosine	SO:0001963
2	"A nucleotide modified by methylation." [SO:ke]	\N	methylated_DNA_base_feature	SOFA	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	401301	SO:0001919	SO:0000114	4_methylcytosine	SO:0000306
2	"A modified cytosine DNA base feature." [SO:ke]	\N	modified_cytosine	\N	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	401302	SO:0001919	SO:0000114	4_methylcytosine	SO:0001963
2	"A nucleotide modified by methylation." [SO:ke]	\N	methylated_DNA_base_feature	SOFA	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	401303	SO:0001920	SO:0000161	N6_methyladenine	SO:0000306
2	"A modified adenine DNA base feature." [SO:ke]	\N	modified_adenine	\N	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	401304	SO:0001920	SO:0000161	N6_methyladenine	SO:0001962
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	401305	SO:0001921	SO:0000149	mitochondrial_contig	SO:0000143
2	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	401306	SO:0001921	SO:0000149	mitochondrial_contig	SO:0000148
2	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	401307	SO:0001921	SO:0000149	mitochondrial_contig	SO:0000353
2	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	401308	SO:0001922	SO:0000148	mitochondrial_supercontig	SO:0000719
2	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	401309	SO:0001922	SO:0000148	mitochondrial_supercontig	SO:0001876
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	401310	SO:0001923	SO:0001927	TERRA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	401311	SO:0001924	SO:0001927	ARRET	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	401312	SO:0001925	SO:0001927	ARIA	SO:0000655
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	\N	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	401313	SO:0001926	SO:0001927	anti_ARRET	SO:0000655
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	SO	401314	SO:0001927	SO:0000655	telomeric_transcript	SO:0000233
2	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	\N	insertion	DBVAR,SOFA	\N	sequence	"A duplication of the distal region of a chromosome." [SO:bm]	SO	401315	SO:0001928	SO:1000035	distal_duplication	SO:0000667
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	401316	SO:0001929	SO:0000150	mitochondrial_DNA_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	401317	SO:0001929	SO:0000150	mitochondrial_DNA_read	SO:0000149
2	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	401318	SO:0001930	SO:0000150	chloroplast_DNA_read	SO:0000143
2	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	\N	contig	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	401319	SO:0001930	SO:0000150	chloroplast_DNA_read	SO:0000149
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]	SO	401320	SO:0001931	SO:0000994	consensus_gDNA	SO:0000001
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]	SO	401321	SO:0001931	SO:0000994	consensus_gDNA	SO:0001410
2	"" []	\N	sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	401322	SO:0001932	SO:0001695	restriction_enzyme_five_prime_single_strand_overhang	SO:0001692
2	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	401323	SO:0001932	SO:0001695	restriction_enzyme_five_prime_single_strand_overhang	SO:0001954
2	"" []	\N	sticky_end_restriction_enzyme_cleavage_site	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	401324	SO:0001933	SO:0001695	restriction_enzyme_three_prime_single_strand_overhang	SO:0001692
2	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	401325	SO:0001933	SO:0001695	restriction_enzyme_three_prime_single_strand_overhang	SO:0001954
2	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]	SO	401326	SO:0001934	SO:0000705	monomeric_repeat	SO:0000657
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	401327	SO:0001935	SO:0001701	H3K20_trimethylation_site	SO:0001700
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	401328	SO:0001936	SO:0001973	H3K36_acetylation_site	SO:0001702
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	401329	SO:0001937	SO:0001702	H2BK12_acetylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	401330	SO:0001938	SO:0001702	H2AK5_acetylation_site	SO:0001700
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	401331	SO:0001939	SO:0001972	H4K12_acetylation_site	SO:0001702
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	401332	SO:0001940	SO:0001702	H2BK120_acetylation_site	SO:0001700
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	401333	SO:0001941	SO:0001972	H4K91_acetylation_site	SO:0001702
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	401334	SO:0001942	SO:0001702	H2BK20_acetylation_site	SO:0001700
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	401335	SO:0001943	SO:0001973	H3K4ac_acetylation_site	SO:0001702
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	401336	SO:0001944	SO:0001702	H2AK9_acetylation_site	SO:0001700
2	"A histone modification where the modification is the acylation of the residue." [SO:ke]	\N	histone_acetylation_site	\N	\N	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	401337	SO:0001945	SO:0001973	H3K56_acetylation_site	SO:0001702
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	401338	SO:0001946	SO:0001702	H2BK15_acetylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	401339	SO:0001947	SO:0001701	H3R2_monomethylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	401340	SO:0001948	SO:0001701	H3R2_dimethylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	401341	SO:0001949	SO:0001701	H4R3_dimethylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	401342	SO:0001950	SO:0001701	H4K4_trimethylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	401343	SO:0001951	SO:0001701	H3K23_dimethylation_site	SO:0001700
2	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	SO	401344	SO:0001952	SO:0001055	promoter_flanking_region	SO:0001679
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]	SO	401345	SO:0001953	SO:0001954	restriction_enzyme_assembly_scar	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region related to restriction enzyme function." [SO:ke]	SO	401346	SO:0001954	SO:0001411	restriction_enzyme_region	SO:0000001
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]	SO	401347	SO:0001955	SO:0000839	protein_stability_element	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]	SO	401348	SO:0001955	SO:0000839	protein_stability_element	SO:0001411
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide_region that  codes for a protease cleavage site." [SO:ke]	SO	401349	SO:0001956	SO:0000839	protease_site	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide_region that  codes for a protease cleavage site." [SO:ke]	SO	401350	SO:0001956	SO:0000839	protease_site	SO:0001411
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	401351	SO:0001958	SO:0000188	lariat_intron	SO:0000835
2	"" []	\N	promoter_element	\N	\N	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	401352	SO:0001959	SO:0001660	TCT_motif	SO:0001659
2	"A nucleotide modified by methylation." [SO:ke]	\N	methylated_DNA_base_feature	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	401353	SO:0001960	SO:0000114	5_hydroxymethylcytosine	SO:0000306
2	"A modified cytosine DNA base feature." [SO:ke]	\N	modified_cytosine	\N	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	401354	SO:0001960	SO:0000114	5_hydroxymethylcytosine	SO:0001963
2	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	401355	SO:0001961	SO:0001963	5_formylcytosine	SO:0000305
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A modified adenine DNA base feature." [SO:ke]	SO	401356	SO:0001962	SO:0000305	modified_adenine	SO:0001236
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified adenine DNA base feature." [SO:ke]	SO	401357	SO:0001962	SO:0000305	modified_adenine	SO:0001720
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A modified cytosine DNA base feature." [SO:ke]	SO	401358	SO:0001963	SO:0000305	modified_cytosine	SO:0001236
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified cytosine DNA base feature." [SO:ke]	SO	401359	SO:0001963	SO:0000305	modified_cytosine	SO:0001720
2	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A modified guanine DNA base feature." [SO:ke]	SO	401360	SO:0001964	SO:0000305	modified_guanine	SO:0001236
2	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified guanine DNA base feature." [SO:ke]	SO	401361	SO:0001964	SO:0000305	modified_guanine	SO:0001720
2	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	401362	SO:0001965	SO:0001964	8_oxoguanine	SO:0000305
2	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	401363	SO:0001966	SO:0001963	5_carboxylcytosine	SO:0000305
2	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	401364	SO:0001967	SO:0001962	8_oxoadenine	SO:0000305
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant of a protein coding gene." [SO:ke]	SO	401365	SO:0001968	SO:0001576	coding_transcript_variant	SO:0001564
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	401366	SO:0001969	SO:0001627	coding_transcript_intron_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	401367	SO:0001969	SO:0001968	coding_transcript_intron_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	401368	SO:0001970	SO:0001619	non_coding_transcript_intron_variant	SO:0001576
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	401369	SO:0001970	SO:0001627	non_coding_transcript_intron_variant	SO:0001576
2	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	\N	nucleotide_binding_site	\N	\N	sequence	"" []	SO	401370	SO:0001971	SO:0001429	zinc_finger_binding_site	SO:0001655
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	401371	SO:0001972	SO:0001702	histone_4_acylation_site	SO:0001700
2	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	401372	SO:0001973	SO:0001702	histone_3_acetylation_site	SO:0001700
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	SO	401373	SO:0001974	SO:0001659	CTCF_binding_site	SO:0000713
2	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]	SO	401374	SO:0001975	SO:0001692	five_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001687
2	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]	SO	401375	SO:0001976	SO:0001692	three_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001687
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	SO	401376	SO:0001977	SO:0000833	ribonuclease_site	SO:0000673
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	SO	401377	SO:0001977	SO:0000833	ribonuclease_site	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A region of  sequence where developer information is encoded." [SO:ke]	SO	401378	SO:0001978	SO:0000804	signature	SO:0000001
2	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A region of  sequence where developer information is encoded." [SO:ke]	SO	401379	SO:0001978	SO:0000804	signature	SO:0001409
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"A motif that affects the stability of RNA." [PMID:22495308, SO:ke]	SO	401380	SO:0001979	SO:0000715	RNA_stability_element	SO:0000714
2	"" []	\N	promoter_element	\N	\N	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	401381	SO:0001980	SO:0001678	G_box	SO:0001659
2	"" []	\N	promoter_element	\N	\N	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	401382	SO:0001981	SO:0001678	L_box	SO:0001659
2	"" []	\N	promoter_element	\N	\N	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	401383	SO:0001982	SO:0001678	I-box	SO:0001659
2	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	401384	SO:0001983	SO:0001623	5_prime_UTR_premature_start_codon_variant	SO:0001622
2	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]	SO	401385	SO:0001984	SO:0005854	silent_mating_type_cassette_array	SO:0005855
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]	SO	401386	SO:0001985	SO:0001411	Okazaki_fragment	SO:0000001
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]	SO	401387	SO:0001986	SO:0001628	upstream_transcript_variant	SO:0001878
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"" []	SO	401388	SO:0001987	SO:0001628	downstream_transcript_variant	SO:0001878
2	"A UTR variant of the 5' UTR." [SO:ke]	\N	5_prime_UTR_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	401389	SO:0001988	SO:0001983	5_prime_UTR_premature_start_codon_gain_variant	SO:0001623
2	"A UTR variant of the 5' UTR." [SO:ke]	\N	5_prime_UTR_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	401390	SO:0001989	SO:0001983	5_prime_UTR_premature_start_codon_loss_variant	SO:0001623
2	"A UTR variant of the 5' UTR." [SO:ke]	\N	5_prime_UTR_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	401391	SO:0001990	SO:0001983	five_prime_UTR_premature_start_codon_location_variant	SO:0001623
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]	SO	401392	SO:0001991	SO:0000994	consensus_AFLP_fragment	SO:0000001
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	\N	sequence	"A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]	SO	401393	SO:0001991	SO:0000994	consensus_AFLP_fragment	SO:0001410
2	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	401394	SO:0001992	SO:0001650	nonsynonymous_variant	SO:0001818
2	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	401395	SO:0001993	SO:0001419	extended_cis_splice_site	SO:0000162
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	401396	SO:0001994	SO:0001014	intron_base_5	SO:0000188
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	401397	SO:0001994	SO:0001014	intron_base_5	SO:0000835
2	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	\N	cis_splice_site	SOFA	\N	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	401398	SO:0001994	SO:0001993	intron_base_5	SO:0001419
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]	SO	401399	SO:0001995	SO:0001568	extended_intronic_splice_region_variant	SO:0001576
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	401400	SO:0001996	SO:0001014	extended_intronic_splice_region	SO:0000188
2	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	401401	SO:0001996	SO:0001014	extended_intronic_splice_region	SO:0000835
2	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	401402	SO:0001997	SO:0000628	subtelomere	SO:0000830
2	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]	SO	401403	SO:0001998	SO:0000696	sgRNA	SO:0000695
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	401404	SO:0001999	SO:0000713	mating_type_region_motif	SO:0000714
2	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	401405	SO:0001999	SO:0001789	mating_type_region_motif	SO:0005855
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	401406	SO:0002000	SO:0001999	W_region	SO:0000713
2	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	\N	mating_type_region	\N	\N	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	401407	SO:0002000	SO:0001999	W_region	SO:0001789
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	401408	SO:0002001	SO:0001999	Y_region	SO:0000713
2	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	\N	mating_type_region	\N	\N	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	401409	SO:0002001	SO:0001999	Y_region	SO:0001789
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	401410	SO:0002002	SO:0001999	Z1_region	SO:0000713
2	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	\N	mating_type_region	\N	\N	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	401411	SO:0002002	SO:0001999	Z1_region	SO:0001789
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	401412	SO:0002003	SO:0001999	Z2_region	SO:0000713
2	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	\N	mating_type_region	\N	\N	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	401413	SO:0002003	SO:0001999	Z2_region	SO:0001789
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	401414	SO:0002004	SO:0000713	ARS_consensus_sequence	SO:0000714
2	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	origin_of_replication	SOFA	SOFA	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	401415	SO:0002004	SO:0000436	ARS_consensus_sequence	SO:0000296
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]	SO	401416	SO:0002005	SO:0000713	DSR_motif	SO:0000714
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	SO	401417	SO:0002006	SO:0001659	zinc_repressed_element	SO:0000713
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	SO	401418	SO:0002007	SO:1000002	MNV	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	SO	401419	SO:0002007	SO:1000002	MNV	SO:0001411
2	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	\N	missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	401420	SO:0002008	SO:0001586	rare_amino_acid_variant	SO:0001583
2	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	\N	non_conservative_missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	401421	SO:0002009	SO:0002008	selenocysteine_loss	SO:0001586
2	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	\N	non_conservative_missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	401422	SO:0002010	SO:0002008	pyrrolysine_loss	SO:0001586
2	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence." [SO:ke]	SO	401423	SO:0002011	SO:0001576	intragenic_variant	SO:0001564
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	401424	SO:0002012	SO:0001582	start_lost	SO:0001580
2	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	401425	SO:0002012	SO:0001992	start_lost	SO:0001650
2	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	401426	SO:0002013	SO:0001623	5_prime_UTR_truncation	SO:0001622
2	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	401427	SO:0002014	SO:0001623	5_prime_UTR_elongation	SO:0001622
2	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	401428	SO:0002015	SO:0001624	3_prime_UTR_truncation	SO:0001622
2	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	401429	SO:0002016	SO:0001624	3_prime_UTR_elongation	SO:0001622
2	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located in a conserved intergenic region, between genes." [SO:ke]	SO	401430	SO:0002017	SO:0001628	conserved_intergenic_variant	SO:0001878
2	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A transcript variant occurring within a conserved region of an intron." [SO:ke]	SO	401431	SO:0002018	SO:0001627	conserved_intron_variant	SO:0001576
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	401432	SO:0002019	SO:0001582	start_retained_variant	SO:0001580
2	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	401433	SO:0002019	SO:0001819	start_retained_variant	SO:0001580
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]	SO	401434	SO:0002020	SO:0000713	boundary_element	SO:0000714
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]	SO	401435	SO:0002021	SO:0000713	mating_type_region_replication_fork_barrier	SO:0000714
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	SO	401436	SO:0002022	SO:0000655	priRNA	SO:0000233
2	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]	SO	401437	SO:0002023	SO:0000324	multiplexing_sequence_identifier	SO:0000696
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	401438	SO:0002024	SO:0001999	W_region	SO:0000713
2	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	\N	mating_type_region	\N	\N	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	401439	SO:0002024	SO:0001999	W_region	SO:0001789
2	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	SO	401440	SO:0002025	SO:0000713	cis_acting_homologous_chromosome_pairing_region	SO:0000714
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	SOFA	sequence	"The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]	SO	401441	SO:0002026	SO:0000842	intein_encoding_region	SO:0000704
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]	SO	401442	SO:0002026	SO:0000842	intein_encoding_region	SO:0001411
2	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	\N	reading_frame	SOFA	SOFA	sequence	"A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]	SO	401443	SO:0002027	SO:0000236	uORF	SO:0000717
2	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	\N	reading_frame	SOFA	SOFA	sequence	"An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]	SO	401444	SO:0002028	SO:0000236	sORF	SO:0000717
2	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	\N	reading_frame	SOFA	SOFA	sequence	"A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]	SO	401445	SO:0002029	SO:0000236	tnaORF	SO:0000717
2	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	401446	SO:0002030	SO:0001999	X_region	SO:0000713
2	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	\N	mating_type_region	\N	\N	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	401447	SO:0002030	SO:0001999	X_region	SO:0001789
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	SO	401448	SO:0002031	SO:0000655	shRNA	SO:0000233
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SO	401449	SO:0005836	SO:0000831	regulatory_region	SO:0001411
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	401450	SO:0005837	SO:0000232	U14_snoRNA_primary_transcript	SO:0000483
2	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	\N	snoRNA	SOFA	SOFA	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	401451	SO:0005841	SO:0000593	methylation_guide_snoRNA	SO:0000275
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	SO	401452	SO:0005843	SO:0000655	rRNA_cleavage_RNA	SO:0000233
2	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	401453	SO:0005845	SO:0000147	exon_of_single_exon_gene	SO:0000833
2	"" []	\N	gene_array_member	\N	\N	sequence	"" []	SO	401454	SO:0005847	SO:0005848	cassette_array_member	SO:0000081
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	401455	SO:0005848	SO:0000081	gene_cassette_member	SO:0000401
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	401456	SO:0005849	SO:0000081	gene_subarray_member	SO:0000401
2	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	\N	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	401457	SO:0005850	SO:0001655	primer_binding_site	SO:0000409
2	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	401458	SO:0005850	SO:0000186	primer_binding_site	SO:0000180
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]	SO	401459	SO:0005851	SO:0005855	gene_array	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]	SO	401460	SO:0005852	SO:0005855	gene_subarray	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]	SO	401461	SO:0005853	SO:0000704	gene_cassette	SO:0001411
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]	SO	401462	SO:0005854	SO:0005855	gene_cassette_array	SO:0001411
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A collection of related genes." [SO:ma]	SO	401463	SO:0005855	SO:0001411	gene_group	SO:0000001
2	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	401464	SO:0005856	SO:0000210	selenocysteine_tRNA_primary_transcript	SO:0000483
2	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	401465	SO:0005857	SO:0000253	selenocysteinyl_tRNA	SO:0000655
2	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]	SO	401466	SO:0005858	SO:0000330	syntenic_region	SO:0001410
2	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	401467	SO:0100001	SO:0001067	biochemical_region_of_peptide	SO:0100021
2	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	401468	SO:0100002	SO:0100001	molecular_contact_region	SO:0001067
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	SO	401469	SO:0100003	SO:0001070	intrinsically_unstructured_polypeptide_region	SO:0000839
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	401470	SO:0100004	SO:0001078	catmat_left_handed_three	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	401471	SO:0100005	SO:0001078	catmat_left_handed_four	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	401472	SO:0100006	SO:0001078	catmat_right_handed_three	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	401473	SO:0100007	SO:0001078	catmat_right_handed_four	SO:0001070
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	401474	SO:0100008	SO:0001078	alpha_beta_motif	SO:0001070
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	401475	SO:0100009	SO:0100011	lipoprotein_signal_peptide	SO:0000839
2	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	401476	SO:0100009	SO:0100011	lipoprotein_signal_peptide	SO:0001063
2	"A comment about the sequence." [SO:ke]	biosapiens	remark	SOFA	SOFA	sequence	"An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]	SO	401477	SO:0100010	SO:0000703	no_output	SO:0000700
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens,SOFA	polypeptide	SOFA	biosapiens,SOFA	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	734468	SO:0100011	SO:0000839	cleaved_peptide_region	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	734469	SO:0100011	SO:0000839	cleaved_peptide_region	SO:0001411
2	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	401480	SO:0100011	SO:0001063	cleaved_peptide_region	SO:0000839
2	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	401481	SO:0100012	SO:0001078	peptide_coil	SO:0001070
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]	SO	401482	SO:0100013	SO:0000839	hydrophobic_region_of_peptide	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]	SO	401483	SO:0100013	SO:0000839	hydrophobic_region_of_peptide	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	1167318	SO:0100014	SO:0100011	n_terminal_region	SO:0000839
4	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	1167319	SO:0100014	SO:0100011	n_terminal_region	SO:0001063
2	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	biosapiens	propeptide	biosapiens	biosapiens,SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	401486	SO:0100014	SO:0000418	n_terminal_region	SO:0001062
2	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	biosapiens	peptide_localization_signal	SOFA	biosapiens,SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	401487	SO:0100014	SO:0000418	n_terminal_region	SO:0001527
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	1167324	SO:0100015	SO:0100011	c_terminal_region	SO:0000839
4	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	1167325	SO:0100015	SO:0100011	c_terminal_region	SO:0001063
2	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	biosapiens	propeptide	biosapiens	biosapiens,SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	401490	SO:0100015	SO:0000418	c_terminal_region	SO:0001062
2	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	biosapiens	peptide_localization_signal	SOFA	biosapiens,SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	401491	SO:0100015	SO:0000418	c_terminal_region	SO:0001527
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	1167330	SO:0100016	SO:0100011	central_hydrophobic_region_of_signal_peptide	SO:0000839
4	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	1167331	SO:0100016	SO:0100011	central_hydrophobic_region_of_signal_peptide	SO:0001063
2	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	biosapiens	propeptide	biosapiens	biosapiens,SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	401494	SO:0100016	SO:0000418	central_hydrophobic_region_of_signal_peptide	SO:0001062
2	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	biosapiens	peptide_localization_signal	SOFA	biosapiens,SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	401495	SO:0100016	SO:0000418	central_hydrophobic_region_of_signal_peptide	SO:0001527
2	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	401496	SO:0100017	SO:0001067	polypeptide_conserved_motif	SO:0100021
2	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	401497	SO:0100018	SO:0100001	polypeptide_binding_motif	SO:0001067
2	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	401498	SO:0100019	SO:0100001	polypeptide_catalytic_motif	SO:0001067
2	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	biosapiens	nucleotide_binding_site	\N	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	401499	SO:0100020	SO:0001429	polypeptide_DNA_contact	SO:0001655
2	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	401500	SO:0100020	SO:0100002	polypeptide_DNA_contact	SO:0100001
2	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	401501	SO:0100021	SO:0000839	polypeptide_conserved_region	SO:0000104
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	401502	SO:0100021	SO:0000839	polypeptide_conserved_region	SO:0001411
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SO	401503	SO:1000002	SO:0001059	substitution	SO:0000110
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SO	401504	SO:1000002	SO:0001411	substitution	SO:0000001
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SOFA	sequence_alteration	SOFA	SOFA	sequence	"When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	401505	SO:1000005	SO:1000002	complex_substitution	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	401506	SO:1000005	SO:1000002	complex_substitution	SO:0001411
2	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SOFA	substitution	SOFA	SOFA	sequence	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SO	401507	SO:1000008	SO:0001483	point_mutation	SO:1000002
2	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	401508	SO:1000009	SO:0001483	transition	SO:1000002
2	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	401509	SO:1000010	SO:1000009	pyrimidine_transition	SO:0001483
2	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transition	\N	\N	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	401510	SO:1000011	SO:1000010	C_to_T_transition	SO:1000009
2	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	\N	pyrimidine_transition	\N	\N	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	401511	SO:1000012	SO:1000011	C_to_T_transition_at_pCpG_site	SO:1000010
2	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transition	\N	\N	sequence	"" []	SO	401512	SO:1000013	SO:1000010	T_to_C_transition	SO:1000009
2	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	401513	SO:1000014	SO:1000009	purine_transition	SO:0001483
2	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transition	\N	\N	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	401514	SO:1000015	SO:1000014	A_to_G_transition	SO:1000009
2	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transition	\N	\N	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	401515	SO:1000016	SO:1000014	G_to_A_transition	SO:1000009
2	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	401516	SO:1000017	SO:0001483	transversion	SO:1000002
2	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	401517	SO:1000018	SO:1000017	pyrimidine_to_purine_transversion	SO:0001483
2	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	401518	SO:1000019	SO:1000018	C_to_A_transversion	SO:1000017
2	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"" []	SO	401519	SO:1000020	SO:1000018	C_to_G_transversion	SO:1000017
2	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"A transversion from T to A." [SO:ke]	SO	401520	SO:1000021	SO:1000018	T_to_A_transversion	SO:1000017
2	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"A transversion from T to G." [SO:ke]	SO	401521	SO:1000022	SO:1000018	T_to_G_transversion	SO:1000017
2	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	401522	SO:1000023	SO:1000017	purine_to_pyrimidine_transversion	SO:0001483
2	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	401523	SO:1000024	SO:1000023	A_to_C_transversion	SO:1000017
2	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	401524	SO:1000025	SO:1000023	A_to_T_transversion	SO:1000017
2	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	401525	SO:1000026	SO:1000023	G_to_C_transversion	SO:1000017
2	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transversion	\N	\N	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	401526	SO:1000027	SO:1000023	G_to_T_transversion	SO:1000017
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	401527	SO:1000028	SO:1000183	intrachromosomal_mutation	SO:0000240
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	401528	SO:1000029	SO:1000028	chromosomal_deletion	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	401529	SO:1000030	SO:1000028	chromosomal_inversion	SO:1000183
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	401530	SO:1000031	SO:1000183	interchromosomal_mutation	SO:0000240
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel]	SO	401531	SO:1000032	SO:0001059	indel	SO:0000110
2	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	SO	401532	SO:1000035	SO:0000667	duplication	SO:0001059
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	DBVAR,SOFA	sequence	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	SO	401533	SO:1000035	SO:0000667	duplication	SO:0001411
2	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR,SOFA	sequence_feature	SOFA	SOFA	sequence	"A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	401534	SO:1000036	SO:0001059	inversion	SO:0000110
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	DBVAR,SOFA	region	SOFA	SOFA	sequence	"A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	401535	SO:1000036	SO:0001411	inversion	SO:0000001
2	"" []	\N	chromosome_variation	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	401536	SO:1000037	SO:1000183	chromosomal_duplication	SO:0000240
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	401537	SO:1000038	SO:1000028	intrachromosomal_duplication	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	401538	SO:1000038	SO:1000037	intrachromosomal_duplication	SO:1000183
2	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	\N	duplication	\N	DBVAR	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	401539	SO:1000039	SO:1000173	direct_tandem_duplication	SO:1000035
2	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	\N	duplication	\N	DBVAR	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	401540	SO:1000040	SO:1000173	inverted_tandem_duplication	SO:1000035
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	401541	SO:1000041	SO:0000453	intrachromosomal_transposition	SO:1000183
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	401542	SO:1000041	SO:1000038	intrachromosomal_transposition	SO:1000028
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	401543	SO:1000041	SO:1000038	intrachromosomal_transposition	SO:1000037
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	734536	SO:1000041	SO:1000028	intrachromosomal_transposition	SO:1000183
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	401545	SO:1000042	SO:1000183	compound_chromosome	SO:0000240
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	401546	SO:1000043	SO:1000044	Robertsonian_fusion	SO:1000031
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	401547	SO:1000044	SO:1000031	chromosomal_translocation	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	401548	SO:1000045	SO:1000028	ring_chromosome	SO:1000183
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	401549	SO:1000046	SO:1000030	pericentric_inversion	SO:1000028
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	401550	SO:1000047	SO:1000030	paracentric_inversion	SO:1000028
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	401551	SO:1000048	SO:1000044	reciprocal_chromosomal_translocation	SO:1000031
2	"" []	\N	chromosome_variation	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	401552	SO:1000136	SO:1000183	autosynaptic_chromosome	SO:0000240
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	401553	SO:1000138	SO:1000042	homo_compound_chromosome	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	401554	SO:1000140	SO:1000042	hetero_compound_chromosome	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	401555	SO:1000141	SO:1000028	chromosome_fission	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	401556	SO:1000142	SO:1000136	dexstrosynaptic_chromosome	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	401557	SO:1000143	SO:1000136	laevosynaptic_chromosome	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	401558	SO:1000144	SO:1000037	free_duplication	SO:1000183
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	401559	SO:1000145	SO:1000045	free_ring_duplication	SO:1000028
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	401560	SO:1000145	SO:1000144	free_ring_duplication	SO:1000037
2	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	401561	SO:1000146	SO:1000183	complex_chromosomal_mutation	SO:0000240
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	401562	SO:1000147	SO:1000029	deficient_translocation	SO:1000028
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	401563	SO:1000147	SO:1000044	deficient_translocation	SO:1000031
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	401564	SO:1000148	SO:1000030	inversion_cum_translocation	SO:1000028
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	401565	SO:1000148	SO:1000044	inversion_cum_translocation	SO:1000031
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	734560	SO:1000148	SO:1000028	inversion_cum_translocation	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	401567	SO:1000149	SO:1000031	bipartite_duplication	SO:1000183
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	401568	SO:1000149	SO:1000038	bipartite_duplication	SO:1000028
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	401569	SO:1000149	SO:1000038	bipartite_duplication	SO:1000037
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	401570	SO:1000150	SO:1000044	cyclic_translocation	SO:1000031
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	401571	SO:1000151	SO:1000030	bipartite_inversion	SO:1000028
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	401572	SO:1000152	SO:1000154	uninverted_insertional_duplication	SO:1000037
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	401573	SO:1000153	SO:1000154	inverted_insertional_duplication	SO:1000037
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	401574	SO:1000154	SO:1000037	insertional_duplication	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	401575	SO:1000155	SO:0000453	interchromosomal_transposition	SO:1000183
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	401576	SO:1000155	SO:1000031	interchromosomal_transposition	SO:1000183
2	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	401577	SO:1000156	SO:1000155	inverted_interchromosomal_transposition	SO:0000453
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	401578	SO:1000156	SO:1000155	inverted_interchromosomal_transposition	SO:1000031
2	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	401579	SO:1000157	SO:1000155	uninverted_interchromosomal_transposition	SO:0000453
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	401580	SO:1000157	SO:1000155	uninverted_interchromosomal_transposition	SO:1000031
2	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	401581	SO:1000158	SO:1000041	inverted_intrachromosomal_transposition	SO:0000453
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	401582	SO:1000158	SO:1000041	inverted_intrachromosomal_transposition	SO:1000028
2	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	401583	SO:1000158	SO:1000041	inverted_intrachromosomal_transposition	SO:1000038
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	401584	SO:1000158	SO:1000148	inverted_intrachromosomal_transposition	SO:1000028
2	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	\N	chromosomal_inversion	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	401585	SO:1000158	SO:1000148	inverted_intrachromosomal_transposition	SO:1000030
2	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	\N	chromosomal_translocation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	401586	SO:1000158	SO:1000148	inverted_intrachromosomal_transposition	SO:1000044
2	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	401587	SO:1000159	SO:1000041	uninverted_intrachromosomal_transposition	SO:0000453
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	401588	SO:1000159	SO:1000041	uninverted_intrachromosomal_transposition	SO:1000028
2	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	401589	SO:1000159	SO:1000041	uninverted_intrachromosomal_transposition	SO:1000038
2	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	401590	SO:1000160	SO:1000154	unoriented_insertional_duplication	SO:1000037
2	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	401591	SO:1000161	SO:1000155	unoriented_interchromosomal_transposition	SO:0000453
2	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	401592	SO:1000161	SO:1000155	unoriented_interchromosomal_transposition	SO:1000031
2	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	\N	chromosomal_transposition	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	401593	SO:1000162	SO:1000041	unoriented_intrachromosomal_transposition	SO:0000453
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	401594	SO:1000162	SO:1000041	unoriented_intrachromosomal_transposition	SO:1000028
2	"A duplication that occurred within a chromosome." [SO:ke]	\N	intrachromosomal_duplication	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	401595	SO:1000162	SO:1000041	unoriented_intrachromosomal_transposition	SO:1000038
2	"" []	\N	chromosome_variation	\N	\N	sequence	"" []	SO	401596	SO:1000170	SO:1000183	uncharacterised_chromosomal_mutation	SO:0000240
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	401597	SO:1000171	SO:1000029	deficient_inversion	SO:1000028
2	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	401598	SO:1000171	SO:1000030	deficient_inversion	SO:1000028
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	734595	SO:1000171	SO:1000028	deficient_inversion	SO:1000183
2	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	DBVAR	insertion	DBVAR,SOFA	\N	sequence	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	SO	401600	SO:1000173	SO:1000035	tandem_duplication	SO:0000667
2	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"" []	SO	401601	SO:1000175	SO:1000170	partially_characterised_chromosomal_mutation	SO:1000183
2	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	401602	SO:1000182	SO:0000240	chromosome_number_variation	SO:0001507
2	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	401603	SO:1000182	SO:0000240	chromosome_number_variation	SO:0001524
2	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"" []	SO	401604	SO:1000183	SO:0000240	chromosome_structure_variation	SO:0001507
2	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"" []	SO	401605	SO:1000183	SO:0000240	chromosome_structure_variation	SO:0001524
2	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is alternatively spliced." [SO:xp]	SO	401606	SO:1001187	SO:0000673	alternatively_spliced_transcript	SO:0000831
2	"" []	\N	gene_attribute	\N	\N	sequence	"A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]	SO	401607	SO:1001188	SO:0000463	encodes_1_polypeptide	SO:0000401
2	"" []	\N	gene_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	SO	401608	SO:1001189	SO:0000463	encodes_greater_than_1_polypeptide	SO:0000401
2	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	\N	encodes_greater_than_1_polypeptide	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]	SO	401609	SO:1001190	SO:1001195	encodes_different_polypeptides_different_stop	SO:1001189
2	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	\N	encodes_greater_than_1_polypeptide	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]	SO	401610	SO:1001191	SO:1001195	encodes_overlapping_peptides_different_start	SO:1001189
2	"A gene that encodes more than one transcript." [SO:ke]	\N	encodes_alternately_spliced_transcripts	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]	SO	401611	SO:1001192	SO:1001189	encodes_disjoint_polypeptides	SO:0000463
2	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	\N	encodes_greater_than_1_polypeptide	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]	SO	401612	SO:1001193	SO:1001195	encodes_overlapping_polypeptides_different_start_and_stop	SO:1001189
2	"A gene that encodes more than one transcript." [SO:ke]	\N	encodes_alternately_spliced_transcripts	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	SO	401613	SO:1001195	SO:1001189	encodes_overlapping_peptides	SO:0000463
2	"A gene located in kinetoplast sequence." [SO:xp]	\N	kinetoplast_gene	\N	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	401614	SO:1001196	SO:0000654	cryptogene	SO:0000089
2	"A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]	\N	maxicircle	\N	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	401615	SO:1001196	SO:0000654	cryptogene	SO:0000742
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	401616	SO:1001196	SO:0001431	cryptogene	SO:0000704
2	"A transcript that is polycistronic." [SO:xp]	\N	polycistronic_transcript	\N	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	401617	SO:1001197	SO:0000079	dicistronic_primary_transcript	SO:0000078
2	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	401618	SO:1001197	SO:0000079	dicistronic_primary_transcript	SO:0000673
2	"A transcript that is polycistronic." [SO:xp]	\N	polycistronic_transcript	\N	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	401619	SO:1001197	SO:0000631	dicistronic_primary_transcript	SO:0000078
2	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	401620	SO:1001197	SO:0000631	dicistronic_primary_transcript	SO:0000185
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	734617	SO:1001197	SO:0000185	dicistronic_primary_transcript	SO:0000673
2	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	401622	SO:1001217	SO:0000081	member_of_regulon	SO:0000401
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	401623	SO:1001246	SO:0000316	CDS_independently_known	SO:0000836
2	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	401624	SO:1001247	SO:1001254	orphan_CDS	SO:0000316
2	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	401625	SO:1001249	SO:1001251	CDS_supported_by_domain_match_data	SO:0000316
2	"A CDS that is predicted." [SO:ke]	\N	CDS_predicted	\N	\N	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	401626	SO:1001249	SO:1001251	CDS_supported_by_domain_match_data	SO:1001254
2	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	401627	SO:1001251	SO:1001254	CDS_supported_by_sequence_similarity_data	SO:0000316
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	734624	SO:1001251	SO:0000316	CDS_supported_by_sequence_similarity_data	SO:0000836
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	401629	SO:1001254	SO:0000316	CDS_predicted	SO:0000836
2	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	401630	SO:1001259	SO:1001251	CDS_supported_by_EST_or_cDNA_data	SO:0000316
2	"A CDS that is predicted." [SO:ke]	\N	CDS_predicted	\N	\N	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	401631	SO:1001259	SO:1001251	CDS_supported_by_EST_or_cDNA_data	SO:1001254
2	"Region in mRNA where ribosome assembles." [SO:ke]	\N	ribosome_entry_site	SOFA	\N	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	401632	SO:1001260	SO:0000243	internal_Shine_Dalgarno_sequence	SO:0000139
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	401633	SO:1001260	SO:1001268	internal_Shine_Dalgarno_sequence	SO:0000836
2	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	401634	SO:1001261	SO:0000234	recoded_mRNA	SO:0000233
2	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	\N	recoded	\N	\N	sequence	"An attribute describing a translational frameshift of -1." [SO:ke]	SO	401635	SO:1001262	SO:0000887	minus_1_translationally_frameshifted	SO:0000881
2	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	\N	recoded	\N	\N	sequence	"An attribute describing a translational frameshift of +1." [SO:ke]	SO	401636	SO:1001263	SO:0000887	plus_1_translationally_frameshifted	SO:0000881
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	401637	SO:1001264	SO:1001261	mRNA_recoded_by_translational_bypass	SO:0000234
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	734638	SO:1001264	SO:0000234	mRNA_recoded_by_translational_bypass	SO:0000233
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	\N	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	401639	SO:1001265	SO:1001261	mRNA_recoded_by_codon_redefinition	SO:0000234
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	734640	SO:1001265	SO:0000234	mRNA_recoded_by_codon_redefinition	SO:0000233
2	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	401641	SO:1001268	SO:0000836	recoding_stimulatory_region	SO:0000234
2	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	401642	SO:1001268	SO:0000836	recoding_stimulatory_region	SO:0000834
2	"First codon to be translated by a ribosome." [SO:ke]	\N	start_codon	SOFA	\N	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	401643	SO:1001269	SO:0000680	four_bp_start_codon	SO:0000318
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	401644	SO:1001271	SO:0001216	archaeal_intron	SO:0000188
2	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	\N	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	401645	SO:1001272	SO:0001216	tRNA_intron	SO:0000188
2	"First codon to be translated by a ribosome." [SO:ke]	\N	start_codon	SOFA	\N	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	401646	SO:1001273	SO:0000680	CTG_start_codon	SO:0000318
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	401647	SO:1001274	SO:1001268	SECIS_element	SO:0000836
2	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]	SO	401648	SO:1001275	SO:0001411	retron	SO:0000001
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	401649	SO:1001277	SO:1001268	three_prime_recoding_site	SO:0000836
2	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	401650	SO:1001279	SO:1001277	three_prime_stem_loop_structure	SO:1001268
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	401651	SO:1001280	SO:1001268	five_prime_recoding_site	SO:0000836
2	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	401652	SO:1001281	SO:1001277	flanking_three_prime_quadruplet_recoding_signal	SO:1001268
2	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	401653	SO:1001282	SO:1001288	UAG_stop_codon_signal	SO:1001268
2	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	401654	SO:1001283	SO:1001288	UAA_stop_codon_signal	SO:1001268
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]	SO	401655	SO:1001284	SO:0005855	regulon	SO:0001411
2	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	401656	SO:1001285	SO:1001288	UGA_stop_codon_signal	SO:1001268
2	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	401657	SO:1001286	SO:1001277	three_prime_repeat_recoding_signal	SO:1001268
2	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	\N	recoding_stimulatory_region	\N	\N	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	401658	SO:1001287	SO:1001277	distant_three_prime_recoding_signal	SO:1001268
2	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	401659	SO:1001288	SO:1001268	stop_codon_signal	SO:0000836
2	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]	SO	401660	SO:2000061	SO:0000695	databank_entry	SO:0001409
2	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	SOFA	sequence	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	SO	401661	SO:3000000	SO:0000842	gene_segment	SO:0000704
2	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	SO	401662	SO:3000000	SO:0000842	gene_segment	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A folded sequence." [SO:ke]	SO	731850	SO:0000002	SO:0000001	sequence_secondary_structure	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]	SO	731851	SO:0000003	SO:0001411	G_quartet	SO:0000001
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"" []	SO	731852	SO:0000004	SO:0000147	interior_coding_exon	SO:0000833
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	731853	SO:0000005	SO:0000657	satellite_DNA	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region amplified by a PCR reaction." [SO:ke]	SO	731854	SO:0000006	SO:0001409	PCR_product	SO:0000001
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	762551	SO:0000007	SO:0000143	read_pair	SO:0001410
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SOFA	ultracontig	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	762552	SO:0000007	SO:0000148	read_pair	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	762553	SO:0000007	SO:0000148	read_pair	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	2165089	SO:0000007	SO:0000353	read_pair	SO:0001248
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	731862	SO:0000010	SO:0000733	protein_coding	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	731863	SO:0000011	SO:0000733	non_protein_coding	SO:0000400
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	SO	731864	SO:0000012	SO:0000185	scRNA_primary_transcript	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SO	731865	SO:0000013	SO:0000233	scRNA	SO:0000673
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	731866	SO:0000014	SO:0001659	INR_motif	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	731867	SO:0000014	SO:0000170	INR_motif	SO:0001203
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	731868	SO:0000015	SO:0001659	DPE_motif	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	731869	SO:0000015	SO:0000170	DPE_motif	SO:0001203
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	731870	SO:0000016	SO:0001659	BREu_motif	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	731871	SO:0000016	SO:0000170	BREu_motif	SO:0001203
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	731872	SO:0000017	SO:0000714	PSE_motif	SO:0001683
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	731873	SO:0000017	SO:0001055	PSE_motif	SO:0001679
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]	SO	731874	SO:0000018	SO:0000001	linkage_group	SO:0000110
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	SO	731875	SO:0000020	SO:0000714	RNA_internal_loop	SO:0001683
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	SO	731876	SO:0000021	SO:0000715	asymmetric_RNA_internal_loop	SO:0000714
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]	SO	731877	SO:0000022	SO:0000714	A_minor_RNA_motif	SO:0001683
3	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	731878	SO:0000023	SO:0000020	K_turn_RNA_motif	SO:0000715
3	"A motif that is active in RNA sequence." [SO:ke]	\N	RNA_motif	SOFA	\N	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	731879	SO:0000024	SO:0000020	sarcin_like_RNA_motif	SO:0000715
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	SO	731880	SO:0000025	SO:0000715	symmetric_RNA_internal_loop	SO:0000714
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"" []	SO	731881	SO:0000026	SO:0000714	RNA_junction_loop	SO:0001683
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"" []	SO	731882	SO:0000027	SO:0000715	RNA_hook_turn	SO:0000714
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	731883	SO:0000028	SO:0001411	base_pair	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]	SO	731884	SO:0000029	SO:0000002	WC_base_pair	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A type of non-canonical base-pairing." [PMID:12177293]	SO	731885	SO:0000030	SO:0000002	sugar_edge_base_pair	SO:0001411
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	731886	SO:0000031	SO:0000695	aptamer	SO:0001409
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]	SO	731887	SO:0000032	SO:0000696	DNA_aptamer	SO:0000695
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	731888	SO:0000033	SO:0000696	RNA_aptamer	SO:0000695
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]	SO	731889	SO:0000034	SO:0000696	morpholino_oligo	SO:0000695
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	731891	SO:0000035	SO:0000834	riboswitch	SO:0000833
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	762555	SO:0000035	SO:0000233	riboswitch	SO:0000673
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	731893	SO:0000036	SO:0000830	matrix_attachment_site	SO:0000340
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	731894	SO:0000036	SO:0000830	matrix_attachment_site	SO:0001411
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	731895	SO:0000037	SO:0001055	locus_control_region	SO:0001679
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A part of a match, for example an hsp from blast is a match_part." [SO:ke]	SO	762556	SO:0000039	SO:0000001	match_part	SO:0000110
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A clone of a DNA region of a genome." [SO:ma]	SO	731898	SO:0000040	SO:0000695	genomic_clone	SO:0001409
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]	SO	731899	SO:0000043	SO:0001411	processed_pseudogene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A pseudogene caused by unequal crossing over at recombination." [SO:ke]	SO	731900	SO:0000044	SO:0000336	pseudogene_by_unequal_crossing_over	SO:0001411
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	SO	731901	SO:0000051	SO:0000695	probe	SO:0001409
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	731902	SO:0000054	SO:0000240	aneuploid	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	731903	SO:0000054	SO:0000240	aneuploid	SO:0001524
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	731904	SO:0000055	SO:1000182	hyperploid	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	731905	SO:0000056	SO:1000182	hypoploid	SO:0000240
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SO	731906	SO:0000057	SO:0001679	operator	SO:0005836
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SOFA	binding_site	biosapiens,SOFA	SOFA	sequence	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SO	731907	SO:0000059	SO:0000410	nuclease_binding_site	SO:0000409
3	"" []	\N	chromosome_variation	\N	\N	sequence	"" []	SO	731908	SO:0000060	SO:1000183	compound_chromosome_arm	SO:0000240
3	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	SO	731909	SO:0000061	SO:0001654	restriction_enzyme_binding_site	SO:0000410
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	1164832	SO:0000062	SO:1000028	deficient_intrachromosomal_transposition	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	731911	SO:0000062	SO:0000453	deficient_intrachromosomal_transposition	SO:1000183
3	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	731912	SO:0000062	SO:1000038	deficient_intrachromosomal_transposition	SO:1000028
3	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	731913	SO:0000062	SO:1000038	deficient_intrachromosomal_transposition	SO:1000037
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	731914	SO:0000063	SO:0000453	deficient_interchromosomal_transposition	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	731915	SO:0000063	SO:1000031	deficient_interchromosomal_transposition	SO:1000183
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	731916	SO:0000065	SO:0000240	free_chromosome_arm	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	731917	SO:0000065	SO:0000240	free_chromosome_arm	SO:0001524
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	731918	SO:0000067	SO:0000733	gene_to_gene_feature	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	SO	731919	SO:0000068	SO:0000401	overlapping	SO:0000733
3	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	SO	731920	SO:0000069	SO:0000067	inside_intron	SO:0000401
3	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]	SO	731921	SO:0000070	SO:0000068	inside_intron_antiparallel	SO:0000067
3	"" []	\N	gene_to_gene_feature	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]	SO	731922	SO:0000071	SO:0000068	inside_intron_parallel	SO:0000067
3	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]	SO	731923	SO:0000073	SO:0000067	five_prime_three_prime_overlap	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]	SO	731924	SO:0000074	SO:0000067	five_prime_five_prime_overlap	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]	SO	731925	SO:0000075	SO:0000067	three_prime_three_prime_overlap	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]	SO	731926	SO:0000076	SO:0000067	three_prime_five_prime_overlap	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]	SO	731927	SO:0000077	SO:0000067	antisense	SO:0000401
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is polycistronic." [SO:xp]	SO	731928	SO:0000078	SO:0000831	polycistronic_transcript	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is dicistronic." [SO:ke]	SO	762557	SO:0000079	SO:0000831	dicistronic_transcript	SO:0001411
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	731931	SO:0000080	SO:0000401	operon_member	SO:0000733
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	731932	SO:0000081	SO:0000733	gene_array_member	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	731933	SO:0000083	SO:0000735	macronuclear_sequence	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	731934	SO:0000084	SO:0000735	micronuclear_sequence	SO:0000400
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from nuclear sequence." [SO:xp]	SO	731935	SO:0000087	SO:0001411	nuclear_gene	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene located in mitochondrial sequence." [SO:xp]	SO	731936	SO:0000088	SO:0001411	mt_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene located in kinetoplast sequence." [SO:xp]	SO	731937	SO:0000089	SO:0000704	kinetoplast_gene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from plastid sequence." [SO:xp]	SO	731938	SO:0000090	SO:0001411	plastid_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from apicoplast sequence." [SO:xp]	SO	731939	SO:0000091	SO:0000704	apicoplast_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from chloroplast sequence." [SO:xp]	SO	731940	SO:0000092	SO:0000704	ct_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from chromoplast_sequence." [SO:xp]	SO	731941	SO:0000093	SO:0000704	chromoplast_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from cyanelle sequence." [SO:xp]	SO	731942	SO:0000094	SO:0000704	cyanelle_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A plastid gene from leucoplast sequence." [SO:xp]	SO	731943	SO:0000095	SO:0000704	leucoplast_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene from proplastid sequence." [SO:ke]	SO	731944	SO:0000096	SO:0000704	proplastid_gene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from nucleomorph sequence." [SO:xp]	SO	731945	SO:0000097	SO:0001411	nucleomorph_gene	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from plasmid sequence." [SO:xp]	SO	731946	SO:0000098	SO:0001411	plasmid_gene	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from proviral sequence." [SO:xp]	SO	731947	SO:0000099	SO:0001411	proviral_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A proviral gene with origin endogenous retrovirus." [SO:xp]	SO	731948	SO:0000100	SO:0000704	endogenous_retroviral_gene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	SO	731949	SO:0000101	SO:0001037	transposable_element	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	SO	731950	SO:0000101	SO:0001037	transposable_element	SO:0001411
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A match to an EST or cDNA sequence." [SO:ke]	SO	731951	SO:0000102	SO:0000343	expressed_sequence_match	SO:0001410
3	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	731952	SO:0000103	SO:0000151	clone_insert_end	SO:0000695
4	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	1164866	SO:0000103	SO:0000695	clone_insert_end	SO:0001409
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	SO	731954	SO:0000104	SO:0000001	polypeptide	SO:0000110
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	SO	731955	SO:0000105	SO:0000340	chromosome_arm	SO:0001235
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	SO	1639790	SO:0000105	SO:0001411	chromosome_arm	SO:0000001
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"" []	SO	731957	SO:0000107	SO:0000441	sequencing_primer	SO:0000696
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA with a frameshift." [SO:xp]	SO	731958	SO:0000108	SO:0000233	mRNA_with_frameshift	SO:0000673
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	1639794	SO:0000111	SO:0001411	transposable_element_gene	SO:0000001
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	731960	SO:0000111	SO:0001039	transposable_element_gene	SO:0001037
3	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	SO	731961	SO:0000112	SO:0000696	primer	SO:0000695
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A viral sequence which has integrated into a host genome." [SO:ke]	SO	731962	SO:0000113	SO:0001037	proviral_region	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A viral sequence which has integrated into a host genome." [SO:ke]	SO	731963	SO:0000113	SO:0001037	proviral_region	SO:0001411
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SOFA	base	SOFA	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	731964	SO:0000114	SO:0000305	methylated_cytosine	SO:0001236
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SOFA	epigenetically_modified_region	SOFA	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	731965	SO:0000114	SO:0000305	methylated_cytosine	SO:0001720
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that is modified by editing." [SO:ke]	SO	731966	SO:0000116	SO:0000733	edited	SO:0000400
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript with a translational frameshift." [SO:xp]	SO	731967	SO:0000118	SO:0000831	transcript_with_translational_frameshift	SO:0001411
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a sequence that is regulated." [SO:ke]	SO	731968	SO:0000119	SO:0000733	regulated	SO:0000400
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	SO	731969	SO:0000120	SO:0000673	protein_coding_primary_transcript	SO:0000831
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	731970	SO:0000121	SO:0000441	forward_primer	SO:0000696
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A folded RNA sequence." [SO:ke]	SO	731971	SO:0000122	SO:0001411	RNA_sequence_secondary_structure	SO:0000001
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated at transcription." [SO:ma]	SO	731972	SO:0000123	SO:0000401	transcriptionally_regulated	SO:0000733
3	"" []	\N	gene_attribute	\N	\N	sequence	"Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]	SO	731973	SO:0000124	SO:0000119	transcriptionally_constitutive	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"An inducer molecule is required for transcription to occur." [SO:ke]	SO	731974	SO:0000125	SO:0000119	transcriptionally_induced	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"A repressor molecule is required for transcription to stop." [SO:ke]	SO	731975	SO:0000126	SO:0000119	transcriptionally_repressed	SO:0000401
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is silenced." [SO:xp]	SO	731976	SO:0000127	SO:0001411	silenced_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is silenced by DNA modification." [SO:xp]	SO	762558	SO:0000128	SO:0001411	gene_silenced_by_DNA_modification	SO:0000001
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced by DNA methylation." [SO:xp]	SO	731979	SO:0000129	SO:0000127	gene_silenced_by_DNA_methylation	SO:0000704
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is silenced by DNA methylation." [SO:xp]	SO	1164890	SO:0000129	SO:0000704	gene_silenced_by_DNA_methylation	SO:0001411
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated after it has been translated." [SO:ke]	SO	731981	SO:0000130	SO:0000401	post_translationally_regulated	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated as it is translated." [SO:ke]	SO	731982	SO:0000131	SO:0000401	translationally_regulated	SO:0000733
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	731983	SO:0000132	SO:0000441	reverse_primer	SO:0000696
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]	SO	731984	SO:0000133	SO:0000733	epigenetically_modified	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	SO	731985	SO:0000134	SO:0000401	genomically_imprinted	SO:0000733
3	"" []	\N	gene_attribute	\N	\N	sequence	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	731986	SO:0000135	SO:0000119	maternally_imprinted	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	731987	SO:0000135	SO:0000133	maternally_imprinted	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	731988	SO:0000136	SO:0000119	paternally_imprinted	SO:0000401
3	"" []	\N	gene_attribute	\N	\N	sequence	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	731989	SO:0000136	SO:0000133	paternally_imprinted	SO:0000401
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]	SO	731990	SO:0000137	SO:0000401	allelically_excluded	SO:0000733
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	SO	731991	SO:0000138	SO:0000704	gene_rearranged_at_DNA_level	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	SO	731992	SO:0000138	SO:0001720	gene_rearranged_at_DNA_level	SO:0001411
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	1173130	SO:0000139	SO:0000234	ribosome_entry_site	SO:0000233
5	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	1173131	SO:0000139	SO:0000834	ribosome_entry_site	SO:0000833
3	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	731995	SO:0000139	SO:0000203	ribosome_entry_site	SO:0000836
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	731996	SO:0000140	SO:0005836	attenuator	SO:0000831
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	731997	SO:0000140	SO:0000233	attenuator	SO:0000673
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	731998	SO:0000141	SO:0005836	terminator	SO:0000831
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164907	SO:0000141	SO:0000831	terminator	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A folded DNA sequence." [SO:ke]	SO	732000	SO:0000142	SO:0001411	DNA_sequence_secondary_structure	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of known length which may be used to manufacture a longer region." [SO:ke]	SO	732001	SO:0000143	SO:0000001	assembly_component	SO:0000110
3	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	732002	SO:0000145	SO:0000851	recoded_codon	SO:0000316
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	732003	SO:0000145	SO:0000851	recoded_codon	SO:0000836
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke]	SO	732004	SO:0000146	SO:0000733	capped	SO:0000400
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SO	732005	SO:0000147	SO:0000673	exon	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SO	1639818	SO:0000147	SO:0001411	exon	SO:0000001
4	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	762559	SO:0000148	SO:0000353	supercontig	SO:0001248
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	2102384	SO:0000149	SO:0001410	contig	SO:0000001
6	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	1644946	SO:0000149	SO:0001248	contig	SO:0001410
3	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	732011	SO:0000149	SO:0000719	contig	SO:0001876
4	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	\N	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	1164918	SO:0000149	SO:0001876	contig	SO:0000353
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	2486342	SO:0000150	SO:0001410	read	SO:0000001
3	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SOFA	ultracontig	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	732015	SO:0000150	SO:0000148	read	SO:0000719
3	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	732016	SO:0000150	SO:0000148	read	SO:0001876
6	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	1805594	SO:0000150	SO:0000353	read	SO:0001248
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SO	732018	SO:0000151	SO:0001409	clone	SO:0000001
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	732019	SO:0000152	SO:0000151	YAC	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	732020	SO:0000152	SO:0001235	YAC	SO:0001411
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	732021	SO:0000153	SO:0000151	BAC	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	732022	SO:0000153	SO:0001235	BAC	SO:0001411
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	732023	SO:0000154	SO:0000151	PAC	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	732024	SO:0000154	SO:0001235	PAC	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	SO	732025	SO:0000155	SO:0001411	plasmid	SO:0000001
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	732026	SO:0000156	SO:0000151	cosmid	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	732027	SO:0000156	SO:0001235	cosmid	SO:0001411
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	732028	SO:0000157	SO:0000151	phagemid	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	732029	SO:0000157	SO:0001235	phagemid	SO:0001411
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	732030	SO:0000158	SO:0000151	fosmid	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	732031	SO:0000158	SO:0001235	fosmid	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The point at which one or more contiguous nucleotides were excised." [SO:ke]	SO	732032	SO:0000159	SO:0000001	deletion	SO:0000110
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SOFA	base	SOFA	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	732033	SO:0000161	SO:0000305	methylated_adenine	SO:0001236
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SOFA	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	732034	SO:0000161	SO:0000305	methylated_adenine	SO:0001720
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	732035	SO:0000162	SO:0000185	splice_site	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	732036	SO:0000162	SO:0000833	splice_site	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	732037	SO:0000162	SO:0000833	splice_site	SO:0001411
3	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	732038	SO:0000163	SO:0000162	five_prime_cis_splice_site	SO:0000835
3	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	732039	SO:0000164	SO:0000162	three_prime_cis_splice_site	SO:0000835
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732040	SO:0000165	SO:0001055	enhancer	SO:0001679
3	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"An enhancer bound by a factor." [SO:xp]	SO	732041	SO:0000166	SO:0000727	enhancer_bound_by_factor	SO:0001055
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SO	732042	SO:0000167	SO:0001679	promoter	SO:0005836
3	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	732043	SO:0000169	SO:0000167	RNApol_I_promoter	SO:0001055
3	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	732044	SO:0000170	SO:0000167	RNApol_II_promoter	SO:0001055
3	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	732045	SO:0000171	SO:0000167	RNApol_III_promoter	SO:0001055
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732046	SO:0000172	SO:0000714	CAAT_signal	SO:0001683
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732047	SO:0000172	SO:0001203	CAAT_signal	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732048	SO:0000173	SO:0000713	GC_rich_promoter_region	SO:0000714
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732049	SO:0000173	SO:0001203	GC_rich_promoter_region	SO:0000167
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	732050	SO:0000174	SO:0001659	TATA_box	SO:0000713
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732051	SO:0000175	SO:0000714	minus_10_signal	SO:0001683
3	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732052	SO:0000175	SO:0000613	minus_10_signal	SO:0000752
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732053	SO:0000175	SO:0000613	minus_10_signal	SO:0001203
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732054	SO:0000176	SO:0000714	minus_35_signal	SO:0001683
3	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732055	SO:0000176	SO:0000613	minus_35_signal	SO:0000752
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732056	SO:0000176	SO:0000613	minus_35_signal	SO:0001203
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A nucleotide match against a sequence from another organism." [SO:ma]	SO	732057	SO:0000177	SO:0000343	cross_genome_match	SO:0001410
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]	SO	732058	SO:0000178	SO:0001411	operon	SO:0000001
3	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	732059	SO:0000179	SO:0000151	clone_insert_start	SO:0000695
4	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	1164965	SO:0000179	SO:0000695	clone_insert_start	SO:0001409
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	SO	732061	SO:0000180	SO:0001039	retrotransposon	SO:0001037
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A match against a translated sequence." [SO:ke]	SO	732062	SO:0000181	SO:0000343	translated_nucleotide_match	SO:0001410
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	SO	732063	SO:0000182	SO:0001039	DNA_transposon	SO:0001037
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of the gene which is not transcribed." [SO:ke]	SO	732064	SO:0000183	SO:0000704	non_transcribed_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of the gene which is not transcribed." [SO:ke]	SO	1164972	SO:0000183	SO:0001411	non_transcribed_region	SO:0000001
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	732066	SO:0000184	SO:0000188	U2_intron	SO:0000835
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SO	732067	SO:0000185	SO:0000831	primary_transcript	SO:0001411
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	732068	SO:0000186	SO:0000101	LTR_retrotransposon	SO:0001039
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732069	SO:0000188	SO:0000185	intron	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732070	SO:0000188	SO:0000833	intron	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732071	SO:0000188	SO:0000833	intron	SO:0001411
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	732072	SO:0000189	SO:0000101	non_LTR_retrotransposon	SO:0001039
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	732073	SO:0000190	SO:0000835	five_prime_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	732074	SO:0000190	SO:0000835	five_prime_intron	SO:0000833
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	732075	SO:0000191	SO:0000835	interior_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	732076	SO:0000191	SO:0000835	interior_intron	SO:0000833
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	732077	SO:0000192	SO:0000835	three_prime_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	732078	SO:0000192	SO:0000835	three_prime_intron	SO:0000833
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]	SO	732079	SO:0000193	SO:0000143	RFLP_fragment	SO:0001410
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	732080	SO:0000194	SO:0000180	LINE_element	SO:0000101
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	732081	SO:0000195	SO:0000833	coding_exon	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	732082	SO:0000195	SO:0000833	coding_exon	SO:0001411
3	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	732083	SO:0000196	SO:0000852	five_prime_coding_exon_coding_region	SO:0000147
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	732084	SO:0000196	SO:0000852	five_prime_coding_exon_coding_region	SO:0000833
3	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	732085	SO:0000196	SO:0000195	five_prime_coding_exon_coding_region	SO:0000147
3	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	732086	SO:0000197	SO:0000852	three_prime_coding_exon_coding_region	SO:0000147
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	732087	SO:0000197	SO:0000852	three_prime_coding_exon_coding_region	SO:0000833
3	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	732088	SO:0000197	SO:0000195	three_prime_coding_exon_coding_region	SO:0000147
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"An exon that does not contain any codons." [SO:ke]	SO	732089	SO:0000198	SO:0000833	noncoding_exon	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An exon that does not contain any codons." [SO:ke]	SO	732090	SO:0000198	SO:0000833	noncoding_exon	SO:0001411
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	732091	SO:0000200	SO:0000147	five_prime_coding_exon	SO:0000833
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	732092	SO:0000201	SO:0000833	interior_exon	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	732093	SO:0000201	SO:0000833	interior_exon	SO:0001411
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	732094	SO:0000202	SO:0000147	three_prime_coding_exon	SO:0000833
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	732095	SO:0000203	SO:0000234	UTR	SO:0000233
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	732096	SO:0000203	SO:0000834	UTR	SO:0000833
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732097	SO:0000204	SO:0000836	five_prime_UTR	SO:0000234
3	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732098	SO:0000204	SO:0000836	five_prime_UTR	SO:0000834
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732099	SO:0000205	SO:0000836	three_prime_UTR	SO:0000234
3	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732100	SO:0000205	SO:0000836	three_prime_UTR	SO:0000834
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	732101	SO:0000206	SO:0000180	SINE_element	SO:0000101
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"" []	SO	732102	SO:0000207	SO:1000002	simple_sequence_length_variation	SO:0001059
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	732103	SO:0000207	SO:1000002	simple_sequence_length_variation	SO:0001411
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	732104	SO:0000208	SO:0000101	terminal_inverted_repeat_element	SO:0001039
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SO	732105	SO:0000209	SO:0000185	rRNA_primary_transcript	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	SO	732106	SO:0000210	SO:0000185	tRNA_primary_transcript	SO:0000673
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	732107	SO:0000211	SO:0000483	alanine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	732108	SO:0000212	SO:0000483	arginine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	732109	SO:0000213	SO:0000483	asparagine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	732110	SO:0000214	SO:0000483	aspartic_acid_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	732111	SO:0000215	SO:0000483	cysteine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	732112	SO:0000216	SO:0000483	glutamic_acid_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	732113	SO:0000217	SO:0000483	glutamine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	732114	SO:0000218	SO:0000483	glycine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	732115	SO:0000219	SO:0000483	histidine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	732116	SO:0000220	SO:0000483	isoleucine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	732117	SO:0000221	SO:0000483	leucine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	732118	SO:0000222	SO:0000483	lysine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	732119	SO:0000223	SO:0000483	methionine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	732120	SO:0000224	SO:0000483	phenylalanine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	732121	SO:0000225	SO:0000483	proline_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	732122	SO:0000226	SO:0000483	serine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	732123	SO:0000227	SO:0000483	threonine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	732124	SO:0000228	SO:0000483	tryptophan_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	732125	SO:0000229	SO:0000483	tyrosine_tRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	732126	SO:0000230	SO:0000483	valine_tRNA_primary_transcript	SO:0000185
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	SO	732127	SO:0000231	SO:0000185	snRNA_primary_transcript	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	SO	732128	SO:0000232	SO:0000185	snoRNA_primary_transcript	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SO	732129	SO:0000233	SO:0000831	mature_transcript	SO:0001411
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SO	732130	SO:0000234	SO:0000673	mRNA	SO:0000831
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SOFA	binding_site	biosapiens,SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	732131	SO:0000235	SO:0000410	TF_binding_site	SO:0000409
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	732132	SO:0000235	SO:0005836	TF_binding_site	SO:0000831
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	SO	732133	SO:0000236	SO:0001410	ORF	SO:0000001
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	732134	SO:0000238	SO:0000101	foldback_element	SO:0001039
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequences extending on either side of a specific region." [SO:ke]	SO	732135	SO:0000239	SO:0000001	flanking_region	SO:0000110
3	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"" []	SO	732136	SO:0000240	SO:0001506	chromosome_variation	SO:0001026
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	732137	SO:0000241	SO:0000836	internal_UTR	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	732138	SO:0000241	SO:0000836	internal_UTR	SO:0000834
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	732139	SO:0000242	SO:0000836	untranslated_region_polycistronic_mRNA	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	732140	SO:0000242	SO:0000836	untranslated_region_polycistronic_mRNA	SO:0000834
3	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	732141	SO:0000243	SO:0000204	internal_ribosome_entry_site	SO:0000203
5	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	1639951	SO:0000243	SO:0000836	internal_ribosome_entry_site	SO:0000234
5	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	1639952	SO:0000243	SO:0000836	internal_ribosome_entry_site	SO:0000834
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]	SO	732144	SO:0000246	SO:0000237	polyadenylated	SO:0000733
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	732145	SO:0000248	SO:0001059	sequence_length_variation	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	732146	SO:0000248	SO:0001411	sequence_length_variation	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post_transcriptionally modified base." [SO:ke]	SO	732147	SO:0000250	SO:0001411	modified_RNA_base_feature	SO:0000001
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SO	732148	SO:0000252	SO:0000233	rRNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SO	732149	SO:0000253	SO:0000233	tRNA	SO:0000673
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	732150	SO:0000254	SO:0000655	alanyl_tRNA	SO:0000233
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	732151	SO:0000255	SO:0000483	rRNA_small_subunit_primary_transcript	SO:0000185
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	732152	SO:0000256	SO:0000655	asparaginyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	732153	SO:0000257	SO:0000655	aspartyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	732154	SO:0000258	SO:0000655	cysteinyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	732155	SO:0000259	SO:0000655	glutaminyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	732156	SO:0000260	SO:0000655	glutamyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	732157	SO:0000261	SO:0000655	glycyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	732158	SO:0000262	SO:0000655	histidyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	732159	SO:0000263	SO:0000655	isoleucyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	732160	SO:0000264	SO:0000655	leucyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	732161	SO:0000265	SO:0000655	lysyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	732162	SO:0000266	SO:0000655	methionyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	732163	SO:0000267	SO:0000655	phenylalanyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	732164	SO:0000268	SO:0000655	prolyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	732165	SO:0000269	SO:0000655	seryl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	732166	SO:0000270	SO:0000655	threonyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	732167	SO:0000271	SO:0000655	tryptophanyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	732168	SO:0000272	SO:0000655	tyrosyl_tRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	732169	SO:0000273	SO:0000655	valyl_tRNA	SO:0000233
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SO	732170	SO:0000274	SO:0000233	snRNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SO	732171	SO:0000275	SO:0000233	snoRNA	SO:0000673
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	732172	SO:0000276	SO:0000655	miRNA	SO:0000233
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is bound by a nucleic acid." [SO:xp]	SO	732173	SO:0000278	SO:0000831	transcript_bound_by_nucleic_acid	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is bound by a protein." [SO:xp]	SO	732174	SO:0000279	SO:0000831	transcript_bound_by_protein	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is engineered." [SO:xp]	SO	732175	SO:0000280	SO:0001411	engineered_gene	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is engineered." [SO:xp]	SO	1165087	SO:0000280	SO:0000001	engineered_gene	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is engineered." [SO:xp]	SO	732177	SO:0000280	SO:0001409	engineered_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	732178	SO:0000281	SO:0000704	engineered_foreign_gene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	732179	SO:0000281	SO:0000804	engineered_foreign_gene	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	732180	SO:0000281	SO:0000804	engineered_foreign_gene	SO:0001409
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	1639983	SO:0000281	SO:0000001	engineered_foreign_gene	SO:0000110
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	732182	SO:0000282	SO:0000234	mRNA_with_minus_1_frameshift	SO:0000233
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	732183	SO:0000283	SO:0000101	engineered_foreign_transposable_element_gene	SO:0001039
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	1165094	SO:0000283	SO:0000704	engineered_foreign_transposable_element_gene	SO:0001411
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	732185	SO:0000283	SO:0000280	engineered_foreign_transposable_element_gene	SO:0000704
3	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	732186	SO:0000283	SO:0000280	engineered_foreign_transposable_element_gene	SO:0000804
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	732187	SO:0000283	SO:0000285	engineered_foreign_transposable_element_gene	SO:0000704
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	732188	SO:0000283	SO:0000805	engineered_foreign_transposable_element_gene	SO:0000001
3	"A region that is engineered." [SO:xp]	\N	engineered_region	\N	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	732189	SO:0000283	SO:0000805	engineered_foreign_transposable_element_gene	SO:0000804
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is foreign." [SO:xp]	SO	732190	SO:0000285	SO:0001411	foreign_gene	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441138	SO:0000286	SO:0001411	long_terminal_repeat	SO:0000001
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732192	SO:0000286	SO:0000180	long_terminal_repeat	SO:0000101
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is a fusion." [SO:xp]	SO	732193	SO:0000287	SO:0001411	fusion_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A fusion gene that is engineered." [SO:xp]	SO	732194	SO:0000288	SO:0000704	engineered_fusion_gene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A fusion gene that is engineered." [SO:xp]	SO	732195	SO:0000288	SO:0000804	engineered_fusion_gene	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A fusion gene that is engineered." [SO:xp]	SO	732196	SO:0000288	SO:0000804	engineered_fusion_gene	SO:0001409
3	"A region of sequence containing one or more repeat units." [SO:ke]	SOFA	repeat_region	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	SO	732197	SO:0000289	SO:0000705	microsatellite	SO:0000657
3	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	\N	tandem_repeat	SOFA	SOFA	sequence	"" []	SO	732198	SO:0000290	SO:0000005	dinucleotide_repeat_microsatellite_feature	SO:0000705
3	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	\N	tandem_repeat	SOFA	SOFA	sequence	"" []	SO	732199	SO:0000291	SO:0000005	trinucleotide_repeat_microsatellite_feature	SO:0000705
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	732200	SO:0000293	SO:0001411	engineered_foreign_repetitive_element	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	1639994	SO:0000293	SO:0000001	engineered_foreign_repetitive_element	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	732202	SO:0000293	SO:0000804	engineered_foreign_repetitive_element	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	732203	SO:0000293	SO:0000804	engineered_foreign_repetitive_element	SO:0001409
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	SO	732204	SO:0000294	SO:0001411	inverted_repeat	SO:0000001
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	732205	SO:0000295	SO:0000188	U12_intron	SO:0000835
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	762561	SO:0000296	SO:0000001	origin_of_replication	SO:0000110
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732208	SO:0000297	SO:0001235	D_loop	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165113	SO:0000297	SO:0001411	D_loop	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	732210	SO:0000298	SO:0000001	recombination_feature	SO:0000110
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	732211	SO:0000299	SO:0000298	specific_recombination_site	SO:0001411
3	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	732212	SO:0000300	SO:0000669	recombination_feature_of_rearranged_gene	SO:0000298
3	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	732213	SO:0000301	SO:0000299	vertebrate_immune_system_gene_recombination_feature	SO:0000669
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732214	SO:0000302	SO:0000301	J_gene_recombination_feature	SO:0000300
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	732215	SO:0000303	SO:0000185	clip	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	732216	SO:0000303	SO:0000833	clip	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	732217	SO:0000303	SO:0000833	clip	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732218	SO:0000305	SO:0001411	modified_DNA_base	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A nucleotide modified by methylation." [SO:ke]	SO	732219	SO:0000306	SO:0001236	methylated_DNA_base_feature	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A nucleotide modified by methylation." [SO:ke]	SO	732220	SO:0000306	SO:0001720	methylated_DNA_base_feature	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]	SO	732221	SO:0000307	SO:0000001	CpG_island	SO:0000110
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Attribute to describe a feature that has been experimentally verified." [SO:ke]	SO	732222	SO:0000312	SO:0000905	experimentally_determined	SO:0000733
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732223	SO:0000313	SO:0000002	stem_loop	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]	SO	732224	SO:0000314	SO:0001411	direct_repeat	SO:0000001
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	732225	SO:0000315	SO:0000185	TSS	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	732226	SO:0000315	SO:0000833	TSS	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	732227	SO:0000315	SO:0000833	TSS	SO:0001411
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	732228	SO:0000316	SO:0000234	CDS	SO:0000233
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	732229	SO:0000316	SO:0000834	CDS	SO:0000833
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	732230	SO:0000317	SO:0000695	cDNA_clone	SO:0001409
3	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SOFA	CDS	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	732231	SO:0000318	SO:0000851	start_codon	SO:0000316
3	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	732232	SO:0000318	SO:0000851	start_codon	SO:0000836
3	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SOFA	CDS	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	732233	SO:0000319	SO:0000851	stop_codon	SO:0000316
3	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	732234	SO:0000319	SO:0000851	stop_codon	SO:0000836
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	732235	SO:0000320	SO:0001056	intronic_splice_enhancer	SO:0001679
3	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	732236	SO:0000320	SO:0000662	intronic_splice_enhancer	SO:0000188
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	1640020	SO:0000320	SO:0000835	intronic_splice_enhancer	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	1640021	SO:0000320	SO:0000835	intronic_splice_enhancer	SO:0000833
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	732239	SO:0000321	SO:0000234	mRNA_with_plus_1_frameshift	SO:0000233
3	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	nucleotide_to_protein_binding_site	SOFA	SOFA	sequence	"" []	SO	732240	SO:0000322	SO:0000059	nuclease_hypersensitive_site	SO:0001654
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	732241	SO:0000323	SO:0000316	coding_start	SO:0000836
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	1165145	SO:0000323	SO:0000836	coding_start	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	1165146	SO:0000323	SO:0000836	coding_start	SO:0000834
3	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SO	732244	SO:0000324	SO:0000695	tag	SO:0001409
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	732245	SO:0000325	SO:0000483	rRNA_large_subunit_primary_transcript	SO:0000185
3	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	SO	732246	SO:0000326	SO:0000696	SAGE_tag	SO:0000695
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	732247	SO:0000327	SO:0000316	coding_end	SO:0000836
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	1165152	SO:0000327	SO:0000836	coding_end	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	1165153	SO:0000327	SO:0000836	coding_end	SO:0000834
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"" []	SO	732250	SO:0000328	SO:0000696	microarray_oligo	SO:0000695
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	732251	SO:0000329	SO:0000234	mRNA_with_plus_2_frameshift	SO:0000233
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	732252	SO:0000330	SO:0000001	conserved_region	SO:0000110
3	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]	SO	732253	SO:0000331	SO:0000696	STS	SO:0000695
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	732254	SO:0000332	SO:0001410	coding_conserved_region	SO:0000001
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	732255	SO:0000333	SO:0000673	exon_junction	SO:0000831
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	732256	SO:0000334	SO:0001410	nc_conserved_region	SO:0000001
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	732257	SO:0000335	SO:0000234	mRNA_with_minus_2_frameshift	SO:0000233
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	732258	SO:0000336	SO:0000001	pseudogene	SO:0000110
3	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]	SO	732259	SO:0000337	SO:0000696	RNAi_reagent	SO:0000695
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	732260	SO:0000338	SO:0000182	MITE	SO:0000101
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region in a genome which promotes recombination." [SO:rd]	SO	732261	SO:0000339	SO:0001411	recombination_hotspot	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SO	732262	SO:0000340	SO:0001411	chromosome	SO:0000001
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SO	732263	SO:0000341	SO:0000340	chromosome_band	SO:0001235
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SO	1640042	SO:0000341	SO:0001411	chromosome_band	SO:0000001
3	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	732265	SO:0000342	SO:0000669	site_specific_recombination_target_region	SO:0000298
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SO	732266	SO:0000343	SO:0000001	match	SO:0000110
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"Region of a transcript that regulates splicing." [SO:ke]	SO	732267	SO:0000344	SO:0001679	splice_enhancer	SO:0005836
3	"A sequence used in experiment." [SO:ke]	SOFA	reagent	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	SO	732268	SO:0000345	SO:0000696	EST	SO:0000695
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	732269	SO:0000346	SO:0000342	loxP_site	SO:0000299
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A match against a nucleotide sequence." [SO:ke]	SO	732270	SO:0000347	SO:0001410	nucleotide_match	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A match against a protein sequence." [SO:ke]	SO	732271	SO:0000349	SO:0001410	protein_match	SO:0000001
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	732272	SO:0000350	SO:0000342	FRT_site	SO:0000299
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]	SO	732273	SO:0000352	SO:0000443	DNA	SO:0000400
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SO	732274	SO:0000353	SO:0001410	sequence_assembly	SO:0000001
3	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	nucleotide_to_protein_binding_site	SOFA	SOFA	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	732275	SO:0000354	SO:0000059	group_1_intron_homing_endonuclease_target_region	SO:0001654
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]	SO	732276	SO:0000355	SO:0001411	haplotype_block	SO:0000001
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb]	SO	732277	SO:0000356	SO:0000443	RNA	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]	SO	732278	SO:0000359	SO:0000733	floxed	SO:0000400
3	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	732279	SO:0000360	SO:0000316	codon	SO:0000836
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	1165179	SO:0000360	SO:0000836	codon	SO:0000234
4	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	1165180	SO:0000360	SO:0000836	codon	SO:0000834
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]	SO	732282	SO:0000361	SO:0000733	FRT_flanked	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]	SO	732283	SO:0000362	SO:0000905	invalidated_by_chimeric_cDNA	SO:0000733
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transgene that is floxed." [SO:xp]	SO	732284	SO:0000363	SO:0000704	floxed_gene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of sequence surrounding a transposable element." [SO:ke]	SO	732285	SO:0000364	SO:0001412	transposable_element_flanking_region	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	SO	732286	SO:0000365	SO:0001037	integron	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	SO	732287	SO:0000365	SO:0001037	integron	SO:0001411
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	732288	SO:0000367	SO:0000342	attI_site	SO:0000299
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	732289	SO:0000367	SO:0001039	attI_site	SO:0001037
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The junction in a genome where a transposable_element has inserted." [SO:ke]	SO	732290	SO:0000368	SO:0000699	transposable_element_insertion_site	SO:0000110
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SO	732291	SO:0000370	SO:0000233	small_regulatory_ncRNA	SO:0000673
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	732292	SO:0000371	SO:0000101	conjugative_transposon	SO:0001039
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	732293	SO:0000372	SO:0000831	enzymatic_RNA	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recombinationally rearranged gene by inversion." [SO:xp]	SO	732294	SO:0000373	SO:0000704	recombinationally_inverted_gene	SO:0001411
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"An RNA with catalytic activity." [SO:ma]	SO	732295	SO:0000374	SO:0000673	ribozyme	SO:0000831
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	732296	SO:0000375	SO:0000252	rRNA_5_8S	SO:0000655
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	732297	SO:0000376	SO:0000655	RNA_6S	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	732298	SO:0000377	SO:0000655	CsrB_RsmB_RNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	732299	SO:0000378	SO:0000655	DsrA_RNA	SO:0000233
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	732300	SO:0000379	SO:0000370	GcvB_RNA	SO:0000655
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	SOFA	sequence_motif	SOFA	SOFA	sequence	"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]	SO	732301	SO:0000380	SO:0000714	hammerhead_ribozyme	SO:0001683
3	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	SOFA	sequence	"" []	SO	732302	SO:0000381	SO:0000588	group_IIA_intron	SO:0000188
3	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	SOFA	sequence	"" []	SO	732303	SO:0000382	SO:0000588	group_IIB_intron	SO:0000188
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	732304	SO:0000383	SO:0000655	MicF_RNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	732305	SO:0000384	SO:0000655	OxyS_RNA	SO:0000233
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SO	732306	SO:0000385	SO:0000233	RNase_MRP_RNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SO	732307	SO:0000386	SO:0000233	RNase_P_RNA	SO:0000673
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	732308	SO:0000387	SO:0000655	RprA_RNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	732309	SO:0000388	SO:0000655	RRE_RNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	732310	SO:0000389	SO:0000655	spot_42_RNA	SO:0000233
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SO	732311	SO:0000390	SO:0000233	telomerase_RNA	SO:0000673
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	732312	SO:0000391	SO:0000655	U1_snRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	732313	SO:0000392	SO:0000655	U2_snRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	732314	SO:0000393	SO:0000655	U4_snRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	732315	SO:0000394	SO:0000655	U4atac_snRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	732316	SO:0000395	SO:0000655	U5_snRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	732317	SO:0000396	SO:0000655	U6_snRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	732318	SO:0000397	SO:0000655	U6atac_snRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	732319	SO:0000398	SO:0000655	U11_snRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	732320	SO:0000399	SO:0000655	U12_snRNA	SO:0000233
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	732321	SO:0000403	SO:0000275	U14_snoRNA	SO:0000655
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SO	732322	SO:0000404	SO:0000233	vault_RNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SO	732323	SO:0000405	SO:0000233	Y_RNA	SO:0000673
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	732324	SO:0000406	SO:0000835	twintron	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	732325	SO:0000406	SO:0000835	twintron	SO:0000833
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	732326	SO:0000407	SO:0000252	rRNA_18S	SO:0000655
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens,SOFA	sequence_feature	SOFA	SOFA	sequence	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SO	732327	SO:0000409	SO:0000001	binding_site	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SO	732328	SO:0000410	SO:0001411	protein_binding_site	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region that rescues." [SO:xp]	SO	732329	SO:0000411	SO:0001409	rescue_region	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]	SO	732330	SO:0000412	SO:0001410	restriction_fragment	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region where the sequence differs from that of a specified sequence." [SO:ke]	SO	732331	SO:0000413	SO:0001410	sequence_difference	SO:0000001
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]	SO	732332	SO:0000414	SO:0000905	invalidated_by_genomic_contamination	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]	SO	732333	SO:0000415	SO:0000905	invalidated_by_genomic_polyA_primed_cDNA	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]	SO	732334	SO:0000416	SO:0000905	invalidated_by_partial_processing	SO:0000733
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	732335	SO:0000417	SO:0000839	polypeptide_domain	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	732336	SO:0000417	SO:0000839	polypeptide_domain	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens,SOFA	polypeptide	SOFA	biosapiens,SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640099	SO:0000418	SO:0000839	signal_peptide	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640100	SO:0000418	SO:0000839	signal_peptide	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732339	SO:0000418	SO:0100011	signal_peptide	SO:0000839
3	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	biosapiens,SOFA	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732340	SO:0000418	SO:0100011	signal_peptide	SO:0001063
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	SOFA	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	762562	SO:0000419	SO:0000104	mature_protein_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens,SOFA	region	SOFA	SOFA	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	1259856	SO:0000419	SO:0001411	mature_protein_region	SO:0000001
3	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"" []	SO	732345	SO:0000420	SO:0000208	five_prime_terminal_inverted_repeat	SO:0000182
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"" []	SO	732346	SO:0000420	SO:0000294	five_prime_terminal_inverted_repeat	SO:0000657
3	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	\N	DNA_transposon	\N	\N	sequence	"" []	SO	732347	SO:0000421	SO:0000208	three_prime_terminal_inverted_repeat	SO:0000182
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"" []	SO	732348	SO:0000421	SO:0000294	three_prime_terminal_inverted_repeat	SO:0000657
3	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	732349	SO:0000422	SO:0000286	U5_LTR_region	SO:0000186
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	732350	SO:0000422	SO:0000286	U5_LTR_region	SO:0000657
3	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	732351	SO:0000422	SO:0000840	U5_LTR_region	SO:0001412
3	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	732352	SO:0000423	SO:0000286	R_LTR_region	SO:0000186
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	732353	SO:0000423	SO:0000286	R_LTR_region	SO:0000657
3	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	732354	SO:0000423	SO:0000840	R_LTR_region	SO:0001412
3	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	732355	SO:0000424	SO:0000286	U3_LTR_region	SO:0000186
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	732356	SO:0000424	SO:0000286	U3_LTR_region	SO:0000657
3	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	732357	SO:0000424	SO:0000840	U3_LTR_region	SO:0001412
3	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	732358	SO:0000425	SO:0000186	five_prime_LTR	SO:0000180
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	732359	SO:0000425	SO:0000657	five_prime_LTR	SO:0001411
3	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	732360	SO:0000426	SO:0000186	three_prime_LTR	SO:0000180
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	732361	SO:0000426	SO:0000657	three_prime_LTR	SO:0001411
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732362	SO:0000427	SO:0000848	R_five_prime_LTR_region	SO:0000286
3	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	732363	SO:0000427	SO:0000848	R_five_prime_LTR_region	SO:0000840
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732364	SO:0000427	SO:0000425	R_five_prime_LTR_region	SO:0000286
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732365	SO:0000428	SO:0000848	U5_five_prime_LTR_region	SO:0000286
3	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	732366	SO:0000428	SO:0000848	U5_five_prime_LTR_region	SO:0000840
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732367	SO:0000428	SO:0000425	U5_five_prime_LTR_region	SO:0000286
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732368	SO:0000429	SO:0000848	U3_five_prime_LTR_region	SO:0000286
3	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	732369	SO:0000429	SO:0000848	U3_five_prime_LTR_region	SO:0000840
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732370	SO:0000429	SO:0000425	U3_five_prime_LTR_region	SO:0000286
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732371	SO:0000430	SO:0000426	R_three_prime_LTR_region	SO:0000286
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732372	SO:0000430	SO:0000848	R_three_prime_LTR_region	SO:0000286
3	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	732373	SO:0000430	SO:0000848	R_three_prime_LTR_region	SO:0000840
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732374	SO:0000431	SO:0000426	U3_three_prime_LTR_region	SO:0000286
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732375	SO:0000431	SO:0000848	U3_three_prime_LTR_region	SO:0000286
3	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	732376	SO:0000431	SO:0000848	U3_three_prime_LTR_region	SO:0000840
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732377	SO:0000432	SO:0000426	U5_three_prime_LTR_region	SO:0000286
3	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	long_terminal_repeat	\N	\N	sequence	"" []	SO	732378	SO:0000432	SO:0000848	U5_three_prime_LTR_region	SO:0000286
3	"A region of a repeated sequence." [SO:ke]	\N	repeat_component	\N	\N	sequence	"" []	SO	732379	SO:0000432	SO:0000848	U5_three_prime_LTR_region	SO:0000840
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	2441225	SO:0000433	SO:0001411	non_LTR_retrotransposon_polymeric_tract	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	732381	SO:0000433	SO:0001412	non_LTR_retrotransposon_polymeric_tract	SO:0000001
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	732382	SO:0000433	SO:0000180	non_LTR_retrotransposon_polymeric_tract	SO:0000101
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]	SO	732383	SO:0000434	SO:0000657	target_site_duplication	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	732384	SO:0000435	SO:0001410	RR_tract	SO:0000001
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	732385	SO:0000435	SO:0000180	RR_tract	SO:0000101
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	SO	732386	SO:0000436	SO:0001235	ARS	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	SO	1165283	SO:0000436	SO:0001411	ARS	SO:0000001
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"" []	SO	732388	SO:0000439	SO:1000028	inverted_ring_chromosome	SO:1000183
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	732389	SO:0000440	SO:0001411	vector_replicon	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	732390	SO:0000440	SO:0000695	vector_replicon	SO:0001409
3	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A single stranded oligonucleotide." [SO:ke]	SO	732391	SO:0000441	SO:0000695	ss_oligo	SO:0001409
3	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A double stranded oligonucleotide." [SO:ke]	SO	732392	SO:0000442	SO:0000695	ds_oligo	SO:0001409
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	732393	SO:0000444	SO:0000147	three_prime_noncoding_exon	SO:0000833
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	732394	SO:0000445	SO:0000147	five_prime_noncoding_exon	SO:0000833
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	732395	SO:0000446	SO:0000835	UTR_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	732396	SO:0000446	SO:0000835	UTR_intron	SO:0000833
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	732397	SO:0000447	SO:0000188	five_prime_UTR_intron	SO:0000835
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	732398	SO:0000448	SO:0000188	three_prime_UTR_intron	SO:0000835
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A sequence of nucleotides or amino acids which, by design, has a \\"random\\" order of components, given a predetermined input frequency of these components." [SO:ma]	SO	732399	SO:0000449	SO:0000443	random_sequence	SO:0000400
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	SO	732400	SO:0000450	SO:0000340	interband	SO:0001235
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	SO	1640156	SO:0000450	SO:0001411	interband	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes a polyadenylated mRNA." [SO:xp]	SO	732402	SO:0000451	SO:0000704	gene_with_polyadenylated_mRNA	SO:0001411
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	732403	SO:0000453	SO:0000240	chromosomal_transposition	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	732404	SO:0000453	SO:0000240	chromosomal_transposition	SO:0001524
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SO	732405	SO:0000454	SO:0000233	rasiRNA	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes an mRNA with a frameshift." [SO:xp]	SO	732406	SO:0000455	SO:0000704	gene_with_mRNA_with_frameshift	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is recombinationally rearranged." [SO:ke]	SO	732407	SO:0000456	SO:0001411	recombinationally_rearranged_gene	SO:0000001
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	732408	SO:0000457	SO:1000183	interchromosomal_duplication	SO:0000240
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732409	SO:0000458	SO:0000301	D_gene_segment	SO:0000300
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene with a transcript that is trans-spliced." [SO:xp]	SO	732410	SO:0000459	SO:0001411	gene_with_trans_spliced_transcript	SO:0000001
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	732411	SO:0000460	SO:0000300	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000299
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	732412	SO:0000461	SO:1000028	inversion_derived_bipartite_deficiency	SO:1000183
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A non-functional descendant of a functional entity." [SO:cjm]	SO	732413	SO:0000462	SO:0000001	pseudogenic_region	SO:0000110
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A gene that encodes more than one transcript." [SO:ke]	SO	732414	SO:0000463	SO:0000733	encodes_alternately_spliced_transcripts	SO:0000400
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A non-functional descendant of an exon." [SO:ke]	SO	732415	SO:0000464	SO:0001411	decayed_exon	SO:0000001
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	732416	SO:0000465	SO:1000028	inversion_derived_deficiency_plus_duplication	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	732417	SO:0000465	SO:1000037	inversion_derived_deficiency_plus_duplication	SO:1000183
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732418	SO:0000466	SO:0000301	V_gene_segment	SO:0000300
3	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]	SO	732419	SO:0000467	SO:0000119	post_translationally_regulated_by_protein_stability	SO:0000401
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	1640171	SO:0000468	SO:0001410	golden_path_fragment	SO:0000001
3	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	732421	SO:0000468	SO:0000353	golden_path_fragment	SO:0001248
3	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]	SO	732422	SO:0000469	SO:0000119	post_translationally_regulated_by_protein_modification	SO:0000401
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732423	SO:0000470	SO:0000301	J_gene_segment	SO:0000300
3	"" []	\N	gene_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation." [SO:ke]	SO	732424	SO:0000471	SO:0000119	autoregulated	SO:0000401
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	SO	732425	SO:0000472	SO:0001248	tiling_path	SO:0001410
3	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	732426	SO:0000473	SO:0000123	negatively_autoregulated	SO:0000119
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	1640177	SO:0000474	SO:0001410	tiling_path_fragment	SO:0000001
3	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	732428	SO:0000474	SO:0000353	tiling_path_fragment	SO:0001248
3	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	732429	SO:0000475	SO:0000123	positively_autoregulated	SO:0000119
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	1165330	SO:0000476	SO:0000143	contig_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	732431	SO:0000476	SO:0000149	contig_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	732432	SO:0000476	SO:0000149	contig_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	732433	SO:0000476	SO:0000149	contig_read	SO:0000353
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732434	SO:0000478	SO:0000301	C_gene_segment	SO:0000300
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is trans-spliced." [SO:xp]	SO	732435	SO:0000479	SO:0000831	trans_spliced_transcript	SO:0001411
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	732436	SO:0000480	SO:0000695	tiling_path_clone	SO:0001409
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	732437	SO:0000480	SO:0000143	tiling_path_clone	SO:0001410
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	732438	SO:0000480	SO:0000472	tiling_path_clone	SO:0000353
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	732439	SO:0000481	SO:0000657	terminal_inverted_repeat	SO:0001411
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	732440	SO:0000481	SO:0000182	terminal_inverted_repeat	SO:0000101
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	732441	SO:0000482	SO:0000300	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000299
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A primary transcript that is never translated into a protein." [SO:ke]	SO	732442	SO:0000483	SO:0000673	nc_primary_transcript	SO:0000831
3	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	732443	SO:0000484	SO:0000852	three_prime_coding_exon_noncoding_region	SO:0000147
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	732444	SO:0000484	SO:0000852	three_prime_coding_exon_noncoding_region	SO:0000833
3	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	732445	SO:0000484	SO:0000195	three_prime_coding_exon_noncoding_region	SO:0000147
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732446	SO:0000485	SO:0000301	DJ_J_cluster	SO:0000300
3	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	732447	SO:0000486	SO:0000852	five_prime_coding_exon_noncoding_region	SO:0000147
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	732448	SO:0000486	SO:0000852	five_prime_coding_exon_noncoding_region	SO:0000833
3	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SOFA	exon	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	732449	SO:0000486	SO:0000195	five_prime_coding_exon_noncoding_region	SO:0000147
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732450	SO:0000487	SO:0000301	VDJ_J_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732451	SO:0000488	SO:0000301	VDJ_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732452	SO:0000489	SO:0000301	VJ_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732453	SO:0000490	SO:0000301	VJ_J_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732454	SO:0000491	SO:0000301	VJ_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	732455	SO:0000492	SO:0000301	D_gene_recombination_feature	SO:0000300
4	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165357	SO:0000493	SO:0000939	three_prime_D_heptamer	SO:0000301
3	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732457	SO:0000493	SO:0000492	three_prime_D_heptamer	SO:0000939
4	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165359	SO:0000494	SO:0000939	three_prime_D_nonamer	SO:0000301
3	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732459	SO:0000494	SO:0000492	three_prime_D_nonamer	SO:0000939
5	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640209	SO:0000495	SO:0000301	three_prime_D_spacer	SO:0000300
3	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732461	SO:0000495	SO:0000492	three_prime_D_spacer	SO:0000939
4	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165363	SO:0000496	SO:0000939	five_prime_D_heptamer	SO:0000301
3	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732463	SO:0000496	SO:0000492	five_prime_D_heptamer	SO:0000939
4	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165365	SO:0000497	SO:0000939	five_prime_D_nonamer	SO:0000301
3	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732465	SO:0000497	SO:0000492	five_prime_D_nonamer	SO:0000939
5	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640213	SO:0000498	SO:0000301	five_prime_D_spacer	SO:0000300
3	"" []	\N	vertebrate_immune_system_gene_recombination_signal_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732467	SO:0000498	SO:0000492	five_prime_D_spacer	SO:0000939
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]	SO	732468	SO:0000499	SO:0001248	virtual_sequence	SO:0001410
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]	SO	732469	SO:0000500	SO:0000002	Hoogsteen_base_pair	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A type of non-canonical base-pairing." [SO:ke]	SO	732470	SO:0000501	SO:0000002	reverse_Hoogsteen_base_pair	SO:0001411
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732471	SO:0000504	SO:0000301	D_DJ_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732472	SO:0000505	SO:0000301	D_DJ_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732473	SO:0000506	SO:0000301	D_DJ_J_C_cluster	SO:0000300
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	762564	SO:0000507	SO:0001411	pseudogenic_exon	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	732475	SO:0000507	SO:0000336	pseudogenic_exon	SO:0001411
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732477	SO:0000508	SO:0000301	D_DJ_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732478	SO:0000509	SO:0000301	D_J_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732479	SO:0000510	SO:0000301	VD_gene_segment	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732480	SO:0000511	SO:0000301	J_C_cluster	SO:0000300
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	732481	SO:0000512	SO:1000028	inversion_derived_deficiency_plus_aneuploid	SO:1000183
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732482	SO:0000513	SO:0000301	J_cluster	SO:0000300
3	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732483	SO:0000514	SO:0000939	J_nonamer	SO:0000301
3	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732484	SO:0000515	SO:0000939	J_heptamer	SO:0000301
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	SO	732485	SO:0000516	SO:0001411	pseudogenic_transcript	SO:0000001
4	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165385	SO:0000517	SO:0000301	J_spacer	SO:0000300
3	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732487	SO:0000517	SO:0000939	J_spacer	SO:0000301
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732488	SO:0000518	SO:0000301	V_DJ_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732489	SO:0000519	SO:0000301	V_DJ_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732490	SO:0000520	SO:0000301	V_VDJ_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732491	SO:0000521	SO:0000301	V_VDJ_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732492	SO:0000522	SO:0000301	V_VDJ_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732493	SO:0000523	SO:0000301	V_VJ_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732494	SO:0000524	SO:0000301	V_VJ_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732495	SO:0000525	SO:0000301	V_VJ_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732496	SO:0000526	SO:0000301	V_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732497	SO:0000527	SO:0000301	V_D_DJ_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732498	SO:0000528	SO:0000301	V_D_DJ_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732499	SO:0000529	SO:0000301	V_D_DJ_J_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732500	SO:0000530	SO:0000301	V_D_DJ_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732501	SO:0000531	SO:0000301	V_D_J_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732502	SO:0000532	SO:0000301	V_D_J_cluster	SO:0000300
3	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732503	SO:0000533	SO:0000939	V_heptamer	SO:0000301
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732504	SO:0000534	SO:0000301	V_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732505	SO:0000535	SO:0000301	V_J_C_cluster	SO:0000300
3	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732506	SO:0000536	SO:0000939	V_nonamer	SO:0000301
4	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165406	SO:0000537	SO:0000301	V_spacer	SO:0000300
3	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732508	SO:0000537	SO:0000939	V_spacer	SO:0000301
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732509	SO:0000538	SO:0000301	V_gene_recombination_feature	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732510	SO:0000539	SO:0000301	DJ_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732511	SO:0000540	SO:0000301	DJ_J_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732512	SO:0000541	SO:0000301	VDJ_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732513	SO:0000542	SO:0000301	V_DJ_C_cluster	SO:0000300
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	732514	SO:0000544	SO:0000101	helitron	SO:0001039
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	732515	SO:0000545	SO:0000002	recoding_pseudoknot	SO:0001411
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	732516	SO:0000545	SO:0000836	recoding_pseudoknot	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	732517	SO:0000545	SO:0000836	recoding_pseudoknot	SO:0000834
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	732518	SO:0000546	SO:0000443	designed_sequence	SO:0000400
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	732519	SO:0000547	SO:1000028	inversion_derived_bipartite_duplication	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	732520	SO:0000547	SO:1000037	inversion_derived_bipartite_duplication	SO:1000183
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes a transcript that is edited." [SO:xp]	SO	732521	SO:0000548	SO:0000704	gene_with_edited_transcript	SO:0001411
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	732522	SO:0000549	SO:1000028	inversion_derived_duplication_plus_aneuploid	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	732523	SO:0000549	SO:1000037	inversion_derived_duplication_plus_aneuploid	SO:1000183
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	732524	SO:0000550	SO:0000240	aneuploid_chromosome	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	732525	SO:0000550	SO:0000240	aneuploid_chromosome	SO:0001524
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732526	SO:0000551	SO:0005836	polyA_signal_sequence	SO:0000831
3	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	732527	SO:0000552	SO:0000204	Shine_Dalgarno_sequence	SO:0000203
5	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	1640268	SO:0000552	SO:0000836	Shine_Dalgarno_sequence	SO:0000234
5	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	1640269	SO:0000552	SO:0000836	Shine_Dalgarno_sequence	SO:0000834
3	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732530	SO:0000553	SO:0000203	polyA_site	SO:0000836
7	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2084227	SO:0000553	SO:0000673	polyA_site	SO:0000831
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732532	SO:0000555	SO:0000835	five_prime_clip	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732533	SO:0000555	SO:0000835	five_prime_clip	SO:0000833
3	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732534	SO:0000556	SO:0000939	five_prime_D_recombination_signal_sequence	SO:0000301
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732535	SO:0000557	SO:0000835	three_prime_clip	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732536	SO:0000557	SO:0000835	three_prime_clip	SO:0000833
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732537	SO:0000558	SO:0000301	C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732538	SO:0000559	SO:0000301	D_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732539	SO:0000560	SO:0000301	D_J_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732540	SO:0000561	SO:0000301	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"" []	SO	732541	SO:0000562	SO:0000301	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000300
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	732542	SO:0000563	SO:0000300	vertebrate_immune_system_gene_recombination_spacer	SO:0000299
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732543	SO:0000564	SO:0000301	V_DJ_J_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732544	SO:0000565	SO:0000301	V_VDJ_J_C_cluster	SO:0000300
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732545	SO:0000566	SO:0000301	V_VJ_J_C_cluster	SO:0000300
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	732546	SO:0000567	SO:1000183	inversion_derived_aneuploid_chromosome	SO:0000240
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	732547	SO:0000568	SO:0001055	bidirectional_promoter	SO:0001679
3	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732548	SO:0000570	SO:0000939	three_prime_D_recombination_signal_sequence	SO:0000301
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732549	SO:0000571	SO:0000401	miRNA_encoding	SO:0000733
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732550	SO:0000572	SO:0000301	DJ_gene_segment	SO:0000300
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732551	SO:0000573	SO:0000401	rRNA_encoding	SO:0000733
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732552	SO:0000574	SO:0000301	VDJ_gene_segment	SO:0000300
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732553	SO:0000575	SO:0000401	scRNA_encoding	SO:0000733
3	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	732554	SO:0000576	SO:0000301	VJ_gene_segment	SO:0000300
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SOFA	chromosome	SOFA	SOFA	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	732555	SO:0000577	SO:0000830	centromere	SO:0000340
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	732556	SO:0000577	SO:0000830	centromere	SO:0001411
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732557	SO:0000578	SO:0000401	snoRNA_encoding	SO:0000733
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A locatable feature on a transcript that is edited." [SO:ma]	SO	732558	SO:0000579	SO:0000673	edited_transcript_feature	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A locatable feature on a transcript that is edited." [SO:ma]	SO	1640299	SO:0000579	SO:0001411	edited_transcript_feature	SO:0000001
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	732560	SO:0000580	SO:0000483	methylation_guide_snoRNA_primary_transcript	SO:0000185
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	732561	SO:0000581	SO:0000001	cap	SO:0000110
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	732562	SO:0000582	SO:0000483	rRNA_cleavage_snoRNA_primary_transcript	SO:0000185
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	732563	SO:0000583	SO:0000833	pre_edited_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	732564	SO:0000583	SO:0000833	pre_edited_region	SO:0001411
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	732565	SO:0000584	SO:0000655	tmRNA	SO:0000233
3	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	732566	SO:0000585	SO:0000011	C_D_box_snoRNA_encoding	SO:0000401
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	SO	732567	SO:0000586	SO:0000185	tmRNA_primary_transcript	SO:0000673
3	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	732568	SO:0000587	SO:0000188	group_I_intron	SO:0000835
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	732569	SO:0000588	SO:0000835	autocatalytically_spliced_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	732570	SO:0000588	SO:0000835	autocatalytically_spliced_intron	SO:0000833
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	SO	732571	SO:0000589	SO:0000185	SRP_RNA_primary_transcript	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SO	732572	SO:0000590	SO:0000233	SRP_RNA	SO:0000673
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]	SO	732573	SO:0000591	SO:0001411	pseudoknot	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]	SO	732574	SO:0000592	SO:0000002	H_pseudoknot	SO:0001411
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	732575	SO:0000593	SO:0000655	C_D_box_snoRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	732576	SO:0000594	SO:0000655	H_ACA_box_snoRNA	SO:0000233
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	732577	SO:0000595	SO:0000483	C_D_box_snoRNA_primary_transcript	SO:0000185
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	732578	SO:0000596	SO:0000483	H_ACA_box_snoRNA_primary_transcript	SO:0000185
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SO	732579	SO:0000602	SO:0000233	guide_RNA	SO:0000673
3	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	732580	SO:0000603	SO:0000188	group_II_intron	SO:0000835
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	732581	SO:0000604	SO:0000833	editing_block	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	732582	SO:0000604	SO:0000833	editing_block	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]	SO	732583	SO:0000605	SO:0000001	intergenic_region	SO:0000110
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	732584	SO:0000606	SO:0000833	editing_domain	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	732585	SO:0000606	SO:0000833	editing_domain	SO:0001411
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	732586	SO:0000607	SO:0000833	unedited_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	732587	SO:0000607	SO:0000833	unedited_region	SO:0001411
3	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	732588	SO:0000608	SO:0000011	H_ACA_box_snoRNA_encoding	SO:0000401
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]	SO	732589	SO:0000609	SO:0000001	oligo_U_tail	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]	SO	732590	SO:0000610	SO:0000001	polyA_sequence	SO:0000110
3	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	intron	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	732591	SO:0000611	SO:0000662	branch_site	SO:0000188
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	1640330	SO:0000611	SO:0000835	branch_site	SO:0000185
5	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	1640331	SO:0000611	SO:0000835	branch_site	SO:0000833
3	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SOFA	intron	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	732594	SO:0000612	SO:0000662	polypyrimidine_tract	SO:0000188
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	1640334	SO:0000612	SO:0000835	polypyrimidine_tract	SO:0000185
5	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	1640335	SO:0000612	SO:0000835	polypyrimidine_tract	SO:0000833
5	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	1640339	SO:0000613	SO:0001679	bacterial_RNApol_promoter	SO:0005836
3	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	732598	SO:0000613	SO:0000167	bacterial_RNApol_promoter	SO:0001055
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	732599	SO:0000614	SO:0000673	bacterial_terminator	SO:0000831
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	732600	SO:0000614	SO:0001679	bacterial_terminator	SO:0005836
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	732601	SO:0000615	SO:0000141	terminator_of_type_2_RNApol_III_promoter	SO:0000673
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	732602	SO:0000615	SO:0000141	terminator_of_type_2_RNApol_III_promoter	SO:0001679
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	732603	SO:0000616	SO:0000185	transcription_end_site	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	732604	SO:0000616	SO:0000833	transcription_end_site	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	732605	SO:0000616	SO:0000833	transcription_end_site	SO:0001411
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"" []	SO	732606	SO:0000617	SO:0001203	RNApol_III_promoter_type_1	SO:0000167
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"" []	SO	732607	SO:0000618	SO:0001203	RNApol_III_promoter_type_2	SO:0000167
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	732608	SO:0000619	SO:0001659	A_box	SO:0000713
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	732609	SO:0000620	SO:0001659	B_box	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	732610	SO:0000620	SO:0000171	B_box	SO:0001203
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"" []	SO	732611	SO:0000621	SO:0001203	RNApol_III_promoter_type_3	SO:0000167
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	732612	SO:0000622	SO:0001659	C_box	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	732613	SO:0000622	SO:0000171	C_box	SO:0001203
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732614	SO:0000623	SO:0000401	snRNA_encoding	SO:0000733
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SOFA	chromosome	SOFA	SOFA	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	732615	SO:0000624	SO:0000830	telomere	SO:0000340
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	732616	SO:0000624	SO:0000830	telomere	SO:0001411
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SOFA	transcription_regulatory_region	SOFA	SOFA	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	732617	SO:0000625	SO:0001055	silencer	SO:0001679
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"" []	SO	732618	SO:0000626	SO:0000340	chromosomal_regulatory_element	SO:0001235
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640357	SO:0000626	SO:0001411	chromosomal_regulatory_element	SO:0000001
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SO	732620	SO:0000627	SO:0001679	insulator	SO:0005836
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"" []	SO	732621	SO:0000628	SO:0000340	chromosomal_structural_element	SO:0001235
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"" []	SO	1640359	SO:0000628	SO:0001411	chromosomal_structural_element	SO:0000001
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"" []	SO	1173133	SO:0000629	SO:0000234	five_prime_open_reading_frame	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	1173134	SO:0000629	SO:0000834	five_prime_open_reading_frame	SO:0000833
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"" []	SO	732625	SO:0000629	SO:0000203	five_prime_open_reading_frame	SO:0000836
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	732626	SO:0000630	SO:0000836	upstream_AUG_codon	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	732627	SO:0000630	SO:0000836	upstream_AUG_codon	SO:0000834
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	732628	SO:0000631	SO:0000673	polycistronic_primary_transcript	SO:0000831
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	732629	SO:0000632	SO:0000673	monocistronic_primary_transcript	SO:0000831
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	732630	SO:0000633	SO:0000233	monocistronic_mRNA	SO:0000673
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	1165531	SO:0000633	SO:0000673	monocistronic_mRNA	SO:0000831
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	1165534	SO:0000634	SO:0000673	polycistronic_mRNA	SO:0000831
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	732633	SO:0000634	SO:0000233	polycistronic_mRNA	SO:0000673
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	SO	732634	SO:0000635	SO:0000673	mini_exon_donor_RNA	SO:0000831
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	732635	SO:0000636	SO:0000185	spliced_leader_RNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	732636	SO:0000636	SO:0000833	spliced_leader_RNA	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	732637	SO:0000636	SO:0000833	spliced_leader_RNA	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A plasmid that is engineered." [SO:xp]	SO	732638	SO:0000637	SO:0001235	engineered_plasmid	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A plasmid that is engineered." [SO:xp]	SO	1640372	SO:0000637	SO:0000001	engineered_plasmid	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid that is engineered." [SO:xp]	SO	732640	SO:0000637	SO:0001409	engineered_plasmid	SO:0000001
3	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	732641	SO:0000638	SO:0000209	transcribed_spacer_region	SO:0000483
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	732642	SO:0000638	SO:0000835	transcribed_spacer_region	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	732643	SO:0000638	SO:0000835	transcribed_spacer_region	SO:0000833
3	"A primary transcript encoding a ribosomal RNA." [SO:ke]	\N	rRNA_primary_transcript	SOFA	\N	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	732644	SO:0000639	SO:0000838	internal_transcribed_spacer_region	SO:0000209
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	732645	SO:0000639	SO:0000838	internal_transcribed_spacer_region	SO:0000835
3	"A primary transcript encoding a ribosomal RNA." [SO:ke]	\N	rRNA_primary_transcript	SOFA	\N	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	732646	SO:0000640	SO:0000838	external_transcribed_spacer_region	SO:0000209
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	\N	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	732647	SO:0000640	SO:0000838	external_transcribed_spacer_region	SO:0000835
3	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	\N	tandem_repeat	SOFA	SOFA	sequence	"" []	SO	732648	SO:0000641	SO:0000005	tetranucleotide_repeat_microsatellite_feature	SO:0000705
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732649	SO:0000642	SO:0000401	SRP_RNA_encoding	SO:0000733
3	"A region of sequence containing one or more repeat units." [SO:ke]	SOFA	repeat_region	SOFA	SOFA	sequence	"A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]	SO	732650	SO:0000643	SO:0000705	minisatellite	SO:0000657
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SO	732651	SO:0000644	SO:0000233	antisense_RNA	SO:0000673
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The reverse complement of the primary transcript." [SO:ke]	SO	732652	SO:0000645	SO:0000673	antisense_primary_transcript	SO:0000831
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SO	732653	SO:0000646	SO:0000233	siRNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a micro RNA." [SO:ke]	SO	732654	SO:0000647	SO:0000185	miRNA_primary_transcript	SO:0000673
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	732655	SO:0000648	SO:0000483	stRNA_primary_transcript	SO:0000185
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SO	732656	SO:0000649	SO:0000233	stRNA	SO:0000673
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	732657	SO:0000650	SO:0000655	small_subunit_rRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	732658	SO:0000651	SO:0000655	large_subunit_rRNA	SO:0000233
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	732659	SO:0000652	SO:0000252	rRNA_5S	SO:0000655
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	732660	SO:0000653	SO:0000252	rRNA_28S	SO:0000655
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	732661	SO:0000654	SO:0000088	maxicircle_gene	SO:0000704
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	732662	SO:0000654	SO:0001235	maxicircle_gene	SO:0001411
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SO	732663	SO:0000655	SO:0000673	ncRNA	SO:0000831
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732664	SO:0000656	SO:0000401	stRNA_encoding	SO:0000733
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of sequence containing one or more repeat units." [SO:ke]	SO	732665	SO:0000657	SO:0000001	repeat_region	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A repeat that is located at dispersed sites in the genome." [SO:ke]	SO	732666	SO:0000658	SO:0001411	dispersed_repeat	SO:0000001
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732667	SO:0000659	SO:0000401	tmRNA_encoding	SO:0000733
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	732668	SO:0000662	SO:0000835	spliceosomal_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	732669	SO:0000662	SO:0000835	spliceosomal_intron	SO:0000833
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732670	SO:0000663	SO:0000401	tRNA_encoding	SO:0000733
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"" []	SO	732671	SO:0000664	SO:0000340	introgressed_chromosome_region	SO:0001235
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640401	SO:0000664	SO:0001411	introgressed_chromosome_region	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is monocistronic." [SO:xp]	SO	732673	SO:0000665	SO:0000831	monocistronic_transcript	SO:0001411
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	732674	SO:0000666	SO:0000835	mobile_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	732675	SO:0000666	SO:0000835	mobile_intron	SO:0000833
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	2452728	SO:0000666	SO:0000001	mobile_intron	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	2441371	SO:0000666	SO:0001411	mobile_intron	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR,SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	SO	732678	SO:0000667	SO:0000001	insertion	SO:0000110
3	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	SOFA	sequence	"A match against an EST sequence." [SO:ke]	SO	732679	SO:0000668	SO:0000347	EST_match	SO:0000343
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	732680	SO:0000669	SO:0001411	sequence_rearrangement_feature	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]	SO	732681	SO:0000670	SO:0000298	chromosome_breakage_sequence	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]	SO	732682	SO:0000671	SO:0000298	internal_eliminated_sequence	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]	SO	732683	SO:0000672	SO:0000298	macronucleus_destined_segment	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SO	732684	SO:0000673	SO:0001411	transcript	SO:0000001
3	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	732685	SO:0000676	SO:0001419	canonical_three_prime_splice_site	SO:0000162
3	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	732686	SO:0000677	SO:0001419	canonical_five_prime_splice_site	SO:0000162
3	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	732687	SO:0000678	SO:0001419	non_canonical_three_prime_splice_site	SO:0000162
3	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	732688	SO:0000679	SO:0001419	non_canonical_five_prime_splice_site	SO:0000162
3	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	732689	SO:0000680	SO:0000360	non_canonical_start_codon	SO:0000851
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons." [SO:ke]	SO	732690	SO:0000681	SO:0000831	aberrant_processed_transcript	SO:0001411
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	732691	SO:0000683	SO:0001056	exonic_splice_enhancer	SO:0001679
3	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SOFA	protein_binding_site	SOFA	SOFA	sequence	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SO	732692	SO:0000684	SO:0001654	nuclease_sensitive_site	SO:0000410
3	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	\N	nuclease_binding_site	SOFA	SOFA	sequence	"" []	SO	732693	SO:0000685	SO:0000684	DNAseI_hypersensitive_site	SO:0000059
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	732694	SO:0000686	SO:1000031	translocation_element	SO:1000183
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]	SO	732695	SO:0000688	SO:0001248	golden_path	SO:0001410
3	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	SOFA	match	SOFA	SOFA	sequence	"A match against cDNA sequence." [SO:ke]	SO	732696	SO:0000689	SO:0000347	cDNA_match	SO:0000343
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes a polycistronic transcript." [SO:xp]	SO	732697	SO:0000690	SO:0001411	gene_with_polycistronic_transcript	SO:0000001
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	1165602	SO:0000691	SO:0000839	cleaved_initiator_methionine	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	1165603	SO:0000691	SO:0000839	cleaved_initiator_methionine	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	732700	SO:0000691	SO:0001063	cleaved_initiator_methionine	SO:0000839
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes a dicistronic transcript." [SO:xp]	SO	732701	SO:0000692	SO:0000704	gene_with_dicistronic_transcript	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes an mRNA that is recoded." [SO:xp]	SO	732702	SO:0000693	SO:0000704	gene_with_recoded_mRNA	SO:0001411
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SOFA	sequence_alteration	SOFA	SOFA	sequence	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SO	732703	SO:0000694	SO:1000002	SNP	SO:0001059
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SO	732704	SO:0000694	SO:1000002	SNP	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence used in experiment." [SO:ke]	SO	732705	SO:0000695	SO:0000001	reagent	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SO	732706	SO:0000696	SO:0001409	oligo	SO:0000001
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	SO	732707	SO:0000697	SO:0001217	gene_with_stop_codon_read_through	SO:0000704
4	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	762565	SO:0000698	SO:0001217	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0000704
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A comment about the sequence." [SO:ke]	SO	732710	SO:0000700	SO:0000001	remark	SO:0000110
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A region of sequence where the validity of the base calling is questionable." [SO:ke]	SO	732711	SO:0000701	SO:0000700	possible_base_call_error	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A region of sequence where there may have been an error in the assembly." [SO:ke]	SO	732712	SO:0000702	SO:0000700	possible_assembly_error	SO:0001410
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of sequence implicated in an experimental result." [SO:ke]	SO	732713	SO:0000703	SO:0001410	experimental_result_region	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	SO	732714	SO:0000704	SO:0000001	gene	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SO	732715	SO:0000705	SO:0001411	tandem_repeat	SO:0000001
3	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	732716	SO:0000706	SO:0000162	trans_splice_acceptor_site	SO:0000835
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	732717	SO:0000707	SO:0000162	trans_splice_donor_site	SO:0000835
3	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	732718	SO:0000708	SO:0001420	SL1_acceptor_site	SO:0000162
3	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	732719	SO:0000709	SO:0001420	SL2_acceptor_site	SO:0000162
3	"" []	\N	protein_coding_gene	\N	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	SO	732720	SO:0000710	SO:0000693	gene_with_stop_codon_redefined_as_selenocysteine	SO:0001217
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene with mRNA recoded by translational bypass." [SO:xp]	SO	762566	SO:0000711	SO:0000704	gene_with_mRNA_recoded_by_translational_bypass	SO:0001411
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene encoding a transcript that has a translational frameshift." [SO:xp]	SO	732723	SO:0000712	SO:0001217	gene_with_transcript_with_translational_frameshift	SO:0000704
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A motif that is active in the DNA form of the sequence." [SO:ke]	SO	732724	SO:0000713	SO:0001683	DNA_motif	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	SO	732725	SO:0000714	SO:0001411	nucleotide_motif	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A motif that is active in RNA sequence." [SO:ke]	SO	732726	SO:0000715	SO:0001683	RNA_motif	SO:0001411
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	732727	SO:0000716	SO:0000078	dicistronic_mRNA	SO:0000673
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	1259874	SO:0000716	SO:0000673	dicistronic_mRNA	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	762567	SO:0000716	SO:0000233	dicistronic_mRNA	SO:0000673
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	SO	732731	SO:0000717	SO:0000001	reading_frame	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]	SO	732732	SO:0000718	SO:0001410	blocked_reading_frame	SO:0000001
3	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SOFA	assembly	SOFA	SOFA	sequence	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SO	732733	SO:0000719	SO:0000353	ultracontig	SO:0001248
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transposable element that is foreign." [SO:ke]	SO	732734	SO:0000720	SO:0001039	foreign_transposable_element	SO:0001037
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes a dicistronic primary transcript." [SO:xp]	SO	732735	SO:0000721	SO:0000690	gene_with_dicistronic_primary_transcript	SO:0000704
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that encodes a polycistronic mRNA." [SO:xp]	SO	732736	SO:0000722	SO:0000690	gene_with_dicistronic_mRNA	SO:0000704
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]	SO	732737	SO:0000723	SO:0001411	iDNA	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732738	SO:0000724	SO:0001235	oriT	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165636	SO:0000724	SO:0001411	oriT	SO:0000001
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens,SOFA	polypeptide	SOFA	biosapiens,SOFA	sequence	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732740	SO:0000725	SO:0000839	transit_peptide	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	732741	SO:0000725	SO:0000839	transit_peptide	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The simplest repeated component of a repeat region. A single repeat." [SO:ke]	SO	732742	SO:0000726	SO:0000001	repeat_unit	SO:0000110
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SO	732743	SO:0000727	SO:0001679	CRM	SO:0005836
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	1165643	SO:0000728	SO:0000839	intein	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	1165644	SO:0000728	SO:0000839	intein	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	732746	SO:0000728	SO:0001063	intein	SO:0000839
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]	SO	732747	SO:0000729	SO:0000401	intein_containing	SO:0000733
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SO	1165647	SO:0000730	SO:0001410	gap	SO:0000001
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SO	732749	SO:0000730	SO:0001248	gap	SO:0001410
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature that is incomplete." [SO:ke]	SO	732750	SO:0000731	SO:0000733	fragmentary	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an unverified region." [SO:ke]	SO	732751	SO:0000732	SO:0000733	predicted	SO:0000400
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	732752	SO:0000734	SO:0000233	exemplar_mRNA	SO:0000673
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	732753	SO:0000737	SO:0000735	mitochondrial_sequence	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	732754	SO:0000738	SO:0000735	nuclear_sequence	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	732755	SO:0000739	SO:0000735	nucleomorphic_sequence	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	732756	SO:0000740	SO:0000735	plastid_sequence	SO:0000400
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]	SO	732757	SO:0000742	SO:0001411	maxicircle	SO:0000001
3	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	732758	SO:0000743	SO:0000736	apicoplast_sequence	SO:0000735
3	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	732759	SO:0000744	SO:0000736	chromoplast_sequence	SO:0000735
3	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	732760	SO:0000745	SO:0000736	chloroplast_sequence	SO:0000735
3	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	732761	SO:0000746	SO:0000736	cyanelle_sequence	SO:0000735
3	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	732762	SO:0000747	SO:0000736	leucoplast_sequence	SO:0000735
3	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	732763	SO:0000748	SO:0000736	proplastid_sequence	SO:0000735
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]	SO	732764	SO:0000750	SO:0001235	amplification_origin	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]	SO	1165656	SO:0000750	SO:0001411	amplification_origin	SO:0000001
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"" []	SO	732766	SO:0000752	SO:0005836	gene_group_regulatory_region	SO:0000831
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SO	762568	SO:0000753	SO:0001409	clone_insert	SO:0000001
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	732769	SO:0000754	SO:0000151	lambda_vector	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	732770	SO:0000754	SO:0001235	lambda_vector	SO:0001411
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"" []	SO	732771	SO:0000755	SO:0000151	plasmid_vector	SO:0000695
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	762569	SO:0000755	SO:0001411	plasmid_vector	SO:0000001
3	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]	SO	732774	SO:0000756	SO:0000348	cDNA	SO:0000443
3	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"" []	SO	732775	SO:0000757	SO:0000352	single_stranded_cDNA	SO:0000348
3	"An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]	\N	nucleic_acid	\N	\N	sequence	"" []	SO	732776	SO:0000758	SO:0000352	double_stranded_cDNA	SO:0000348
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	732777	SO:0000766	SO:0000655	pyrrolysyl_tRNA	SO:0000233
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A plasmid that may integrate with a chromosome." [SO:ma]	SO	732778	SO:0000768	SO:0001235	episome	SO:0001411
3	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	732779	SO:0000769	SO:0000584	tmRNA_coding_piece	SO:0000370
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	732780	SO:0000769	SO:0000834	tmRNA_coding_piece	SO:0000833
3	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	\N	small_regulatory_ncRNA	SOFA	\N	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	732781	SO:0000770	SO:0000584	tmRNA_acceptor_piece	SO:0000370
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	732782	SO:0000770	SO:0000834	tmRNA_acceptor_piece	SO:0000833
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]	SO	732783	SO:0000771	SO:0000001	QTL	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	SO	732784	SO:0000772	SO:0001037	genomic_island	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	SO	732785	SO:0000772	SO:0001037	genomic_island	SO:0001411
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	SO	732786	SO:0000773	SO:0001039	pathogenic_island	SO:0001037
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	732787	SO:0000774	SO:0001039	metabolic_island	SO:0001037
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	SO	732788	SO:0000775	SO:0001039	adaptive_island	SO:0001037
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	732789	SO:0000776	SO:0001039	symbiosis_island	SO:0001037
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A non functional descendant of an rRNA." [SO:ke]	SO	732790	SO:0000777	SO:0001411	pseudogenic_rRNA	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A non functional descendent of a tRNA." [SO:ke]	SO	732791	SO:0000778	SO:0001411	pseudogenic_tRNA	SO:0000001
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"An episome that is engineered." [SO:xp]	SO	732792	SO:0000779	SO:0000155	engineered_episome	SO:0001235
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"An episome that is engineered." [SO:xp]	SO	732793	SO:0000779	SO:0000804	engineered_episome	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"An episome that is engineered." [SO:xp]	SO	732794	SO:0000779	SO:0000804	engineered_episome	SO:0001409
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1173135	SO:0000785	SO:0001409	cloned_region	SO:0000001
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"" []	SO	732796	SO:0000785	SO:0000151	cloned_region	SO:0000695
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature that has been proven." [SO:ke]	SO	732798	SO:0000789	SO:0000733	validated	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a feature that is invalidated." [SO:ke]	SO	732799	SO:0000790	SO:0000733	invalidated	SO:0000400
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A rescue region that is engineered." [SO:xp]	SO	732800	SO:0000794	SO:0000695	engineered_rescue_region	SO:0001409
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A rescue region that is engineered." [SO:xp]	SO	1259883	SO:0000794	SO:0000001	engineered_rescue_region	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A rescue region that is engineered." [SO:xp]	SO	1165692	SO:0000794	SO:0001409	engineered_rescue_region	SO:0000001
3	"A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]	\N	reading_frame	SOFA	SOFA	sequence	"A mini_gene that rescues." [SO:xp]	SO	732803	SO:0000795	SO:0000236	rescue_mini_gene	SO:0000717
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	SO	732804	SO:0000796	SO:0001039	transgenic_transposable_element	SO:0001037
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	732805	SO:0000797	SO:0001039	natural_transposable_element	SO:0001037
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	1165697	SO:0000797	SO:0001037	natural_transposable_element	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	1165698	SO:0000797	SO:0001037	natural_transposable_element	SO:0001411
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	732808	SO:0000798	SO:0001039	engineered_transposable_element	SO:0001037
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	2081476	SO:0000798	SO:0000001	engineered_transposable_element	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	732810	SO:0000798	SO:0001409	engineered_transposable_element	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	732812	SO:0000799	SO:0000804	engineered_foreign_transposable_element	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	732813	SO:0000799	SO:0000804	engineered_foreign_transposable_element	SO:0001409
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	2279406	SO:0000799	SO:0000001	engineered_foreign_transposable_element	SO:0000110
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	762571	SO:0000799	SO:0001039	engineered_foreign_transposable_element	SO:0001037
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	732816	SO:0000800	SO:0000240	assortment_derived_duplication	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	732817	SO:0000800	SO:0000240	assortment_derived_duplication	SO:0001524
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	732818	SO:0000801	SO:0000240	assortment_derived_deficiency_plus_duplication	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	732819	SO:0000801	SO:0000240	assortment_derived_deficiency_plus_duplication	SO:0001524
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	732820	SO:0000802	SO:0000240	assortment_derived_deficiency	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	732821	SO:0000802	SO:0000240	assortment_derived_deficiency	SO:0001524
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	732822	SO:0000803	SO:0000240	assortment_derived_aneuploid	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	732823	SO:0000803	SO:0000240	assortment_derived_aneuploid	SO:0001524
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region that is engineered and foreign." [SO:xp]	SO	732826	SO:0000805	SO:0001409	engineered_foreign_region	SO:0000001
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A tag that is engineered." [SO:xp]	SO	732827	SO:0000807	SO:0000696	engineered_tag	SO:0000695
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tag that is engineered." [SO:xp]	SO	1679587	SO:0000807	SO:0000001	engineered_tag	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tag that is engineered." [SO:xp]	SO	1640498	SO:0000807	SO:0001409	engineered_tag	SO:0000001
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A cDNA clone that has been validated." [SO:xp]	SO	732830	SO:0000808	SO:0000151	validated_cDNA_clone	SO:0000695
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A cDNA clone that is invalid." [SO:xp]	SO	732831	SO:0000809	SO:0000151	invalidated_cDNA_clone	SO:0000695
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A cDNA clone invalidated because it is chimeric." [SO:xp]	SO	732832	SO:0000810	SO:0000317	chimeric_cDNA_clone	SO:0000151
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A cDNA clone invalidated by genomic contamination." [SO:xp]	SO	732833	SO:0000811	SO:0000317	genomically_contaminated_cDNA_clone	SO:0000151
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A cDNA clone invalidated by polyA priming." [SO:xp]	SO	732834	SO:0000812	SO:0000317	polyA_primed_cDNA_clone	SO:0000151
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A cDNA invalidated clone by partial processing." [SO:xp]	SO	732835	SO:0000813	SO:0000317	partially_processed_cDNA_clone	SO:0000151
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]	SO	732836	SO:0000815	SO:0000717	mini_gene	SO:0001410
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that rescues." [SO:xp]	SO	732837	SO:0000816	SO:0001411	rescue_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that rescues." [SO:xp]	SO	762572	SO:0000818	SO:0001411	wild_type_rescue_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in a mitochondria." [SO:xp]	SO	732840	SO:0000819	SO:0001235	mitochondrial_chromosome	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in a chloroplast." [SO:xp]	SO	732841	SO:0000820	SO:0001235	chloroplast_chromosome	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in a chromoplast." [SO:xp]	SO	732842	SO:0000821	SO:0001235	chromoplast_chromosome	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in a cyanelle." [SO:xp]	SO	732843	SO:0000822	SO:0001235	cyanelle_chromosome	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome with origin in a leucoplast." [SO:xp]	SO	732844	SO:0000823	SO:0001235	leucoplast_chromosome	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in a macronucleus." [SO:xp]	SO	732845	SO:0000824	SO:0001235	macronuclear_chromosome	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in a micronucleus." [SO:xp]	SO	732846	SO:0000825	SO:0001235	micronuclear_chromosome	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in a nucleus." [SO:xp]	SO	732847	SO:0000828	SO:0001235	nuclear_chromosome	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in a nucleomorph." [SO:xp]	SO	732848	SO:0000829	SO:0001235	nucleomorphic_chromosome	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of a chromosome." [SO:ke]	SO	1173136	SO:0000830	SO:0000001	chromosome_part	SO:0000110
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a chromosome." [SO:ke]	SO	732850	SO:0000830	SO:0001235	chromosome_part	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of a gene." [SO:ke]	SO	732851	SO:0000831	SO:0000001	gene_member_region	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of a transcript." [SO:ke]	SO	1173137	SO:0000833	SO:0000001	transcript_region	SO:0000110
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a transcript." [SO:ke]	SO	732853	SO:0000833	SO:0000831	transcript_region	SO:0001411
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of a mature transcript." [SO:ke]	SO	732854	SO:0000834	SO:0000673	mature_transcript_region	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of a mature transcript." [SO:ke]	SO	1640515	SO:0000834	SO:0001411	mature_transcript_region	SO:0000001
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	732856	SO:0000835	SO:0000673	primary_transcript_region	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	1640516	SO:0000835	SO:0001411	primary_transcript_region	SO:0000001
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	732858	SO:0000836	SO:0000833	mRNA_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	732859	SO:0000836	SO:0000833	mRNA_region	SO:0001411
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	732860	SO:0000836	SO:0000233	mRNA_region	SO:0000673
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	732861	SO:0000837	SO:0000234	UTR_region	SO:0000233
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	732862	SO:0000837	SO:0000834	UTR_region	SO:0000833
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	1165750	SO:0000838	SO:0000185	rRNA_primary_transcript_region	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	732864	SO:0000838	SO:0000833	rRNA_primary_transcript_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	732865	SO:0000838	SO:0000833	rRNA_primary_transcript_region	SO:0001411
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	732866	SO:0000838	SO:0000483	rRNA_primary_transcript_region	SO:0000185
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens,SOFA	sequence_feature	SOFA	SOFA	sequence	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	SO	762573	SO:0000839	SO:0000001	polypeptide_region	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a repeated sequence." [SO:ke]	SO	732869	SO:0000840	SO:0000001	repeat_component	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	1173138	SO:0000841	SO:0000185	spliceosomal_intron_region	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	1173139	SO:0000841	SO:0000833	spliceosomal_intron_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	1173140	SO:0000841	SO:0000833	spliceosomal_intron_region	SO:0001411
3	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	732873	SO:0000841	SO:0000188	spliceosomal_intron_region	SO:0000835
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"" []	SO	762574	SO:0000842	SO:0000001	gene_component_region	SO:0000110
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	732876	SO:0000847	SO:0000833	tmRNA_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	732877	SO:0000847	SO:0000833	tmRNA_region	SO:0001411
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	732878	SO:0000847	SO:0000370	tmRNA_region	SO:0000655
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	732879	SO:0000848	SO:0001412	LTR_component	SO:0000001
3	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	732880	SO:0000848	SO:0000186	LTR_component	SO:0000180
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	732881	SO:0000848	SO:0000657	LTR_component	SO:0001411
3	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	732882	SO:0000849	SO:0000286	three_prime_LTR_component	SO:0000186
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	732883	SO:0000849	SO:0000286	three_prime_LTR_component	SO:0000657
3	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	732884	SO:0000849	SO:0000840	three_prime_LTR_component	SO:0001412
3	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	732885	SO:0000850	SO:0000286	five_prime_LTR_component	SO:0000186
3	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	732886	SO:0000850	SO:0000286	five_prime_LTR_component	SO:0000657
3	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	732887	SO:0000850	SO:0000840	five_prime_LTR_component	SO:0001412
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	762575	SO:0000851	SO:0000234	CDS_region	SO:0000233
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	762576	SO:0000851	SO:0000834	CDS_region	SO:0000833
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	762577	SO:0000852	SO:0000673	exon_region	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	1805646	SO:0000852	SO:0001411	exon_region	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region that is homologous to another region." [SO:ke]	SO	732896	SO:0000853	SO:0001410	homologous_region	SO:0000001
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A homologous_region that is paralogous to another region." [SO:ke]	SO	732897	SO:0000854	SO:0000330	paralogous_region	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A homologous_region that is orthologous to another region." [SO:ke]	SO	732898	SO:0000855	SO:0000330	orthologous_region	SO:0001410
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Similarity due to common ancestry." [SO:ke]	SO	732899	SO:0000857	SO:0000733	homologous	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]	SO	732900	SO:0000858	SO:0000856	orthologous	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]	SO	732901	SO:0000859	SO:0000856	paralogous	SO:0000733
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]	SO	732902	SO:0000860	SO:0000733	syntenic	SO:0000400
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript that is capped." [SO:xp]	SO	732903	SO:0000861	SO:0000673	capped_primary_transcript	SO:0000831
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA that is capped." [SO:xp]	SO	732904	SO:0000862	SO:0000233	capped_mRNA	SO:0000673
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an mRNA feature." [SO:ke]	SO	732905	SO:0000863	SO:0000733	mRNA_attribute	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]	SO	732906	SO:0000864	SO:0000237	exemplar	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	SO	732907	SO:0000865	SO:0000237	frameshift	SO:0000733
3	"" []	\N	transcript_attribute	\N	\N	sequence	"A frameshift caused by deleting one base." [SO:ke]	SO	732908	SO:0000866	SO:0000863	minus_1_frameshift	SO:0000237
3	"" []	\N	transcript_attribute	\N	\N	sequence	"A frameshift caused by deleting two bases." [SO:ke]	SO	732909	SO:0000867	SO:0000863	minus_2_frameshift	SO:0000237
3	"" []	\N	transcript_attribute	\N	\N	sequence	"A frameshift caused by inserting one base." [SO:ke]	SO	732910	SO:0000868	SO:0000863	plus_1_frameshift	SO:0000237
3	"" []	\N	transcript_attribute	\N	\N	sequence	"A frameshift caused by inserting two bases." [SO:ke]	SO	732911	SO:0000869	SO:0000863	plus_2_framshift	SO:0000237
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]	SO	732912	SO:0000870	SO:0000733	trans_spliced	SO:0000400
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA that is polyadenylated." [SO:xp]	SO	732913	SO:0000871	SO:0000233	polyadenylated_mRNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	732914	SO:0000872	SO:0000233	trans_spliced_mRNA	SO:0000673
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	1165786	SO:0000872	SO:0000673	trans_spliced_mRNA	SO:0000831
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is edited." [SO:ke]	SO	732916	SO:0000873	SO:0000831	edited_transcript	SO:0001411
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that has been edited by A to I substitution." [SO:ke]	SO	732917	SO:0000874	SO:0000673	edited_transcript_by_A_to_I_substitution	SO:0000831
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that is bound by a protein." [SO:ke]	SO	732918	SO:0000875	SO:0000733	bound_by_protein	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]	SO	732919	SO:0000876	SO:0000733	bound_by_nucleic_acid	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]	SO	732920	SO:0000877	SO:0000733	alternatively_spliced	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for one gene product." [SO:ke]	SO	732921	SO:0000878	SO:0000733	monocistronic	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for two gene products." [SO:ke]	SO	732922	SO:0000879	SO:0000237	dicistronic	SO:0000733
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]	SO	732923	SO:0000880	SO:0000733	polycistronic	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	SO	732924	SO:0000881	SO:0000237	recoded	SO:0000733
3	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing the alteration of codon meaning." [SO:ke]	SO	732925	SO:0000882	SO:0000863	codon_redefined	SO:0000237
3	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	732926	SO:0000883	SO:0000360	stop_codon_read_through	SO:0000851
3	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	\N	codon	SOFA	\N	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	732927	SO:0000884	SO:0000145	stop_codon_redefined_as_pyrrolysine	SO:0000360
3	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	\N	codon	SOFA	\N	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	732928	SO:0000885	SO:0000145	stop_codon_redefined_as_selenocysteine	SO:0000360
3	"" []	\N	transcript_attribute	\N	\N	sequence	"Recoded mRNA where a block of nucleotides is not translated." [SO:ke]	SO	732929	SO:0000886	SO:0000863	recoded_by_translational_bypass	SO:0000237
3	"" []	\N	transcript_attribute	\N	\N	sequence	"Recoding by frameshifting a particular site." [SO:ke]	SO	732930	SO:0000887	SO:0000863	translationally_frameshifted	SO:0000237
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	732932	SO:0000888	SO:0001720	maternally_imprinted_gene	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	762579	SO:0000888	SO:0001411	maternally_imprinted_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	732935	SO:0000889	SO:0001720	paternally_imprinted_gene	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	762580	SO:0000889	SO:0001411	paternally_imprinted_gene	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is post translationally regulated." [SO:xp]	SO	732937	SO:0000890	SO:0001411	post_translationally_regulated_gene	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is negatively autoreguated." [SO:xp]	SO	732938	SO:0000891	SO:0001411	negatively_autoregulated_gene	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is positively autoregulated." [SO:xp]	SO	732939	SO:0000892	SO:0001411	positively_autoregulated_gene	SO:0000001
3	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	SO	732940	SO:0000893	SO:0000123	silenced	SO:0000119
3	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	SO	732941	SO:0000894	SO:0000126	silenced_by_DNA_modification	SO:0000123
3	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	732942	SO:0000895	SO:0000893	silenced_by_DNA_methylation	SO:0000126
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is translationally regulated." [SO:xp]	SO	732943	SO:0000896	SO:0001411	translationally_regulated_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is allelically_excluded." [SO:xp]	SO	732944	SO:0000897	SO:0000704	allelically_excluded_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is allelically_excluded." [SO:xp]	SO	732945	SO:0000897	SO:0001720	allelically_excluded_gene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is epigenetically modified." [SO:ke]	SO	732946	SO:0000898	SO:0001411	epigenetically_modified_gene	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]	SO	732947	SO:0000902	SO:0001411	transgene	SO:0000001
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	732948	SO:0000903	SO:0000735	endogenous_retroviral_sequence	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]	SO	732949	SO:0000904	SO:0000401	rearranged_at_DNA_level	SO:0000733
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Attribute to describe a feature that is independently known - not predicted." [SO:ke]	SO	732950	SO:0000906	SO:0000733	independently_known	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]	SO	732951	SO:0000907	SO:0000905	supported_by_sequence_similarity	SO:0000733
3	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]	SO	732952	SO:0000908	SO:0000732	supported_by_domain_match	SO:0000905
3	"An attribute describing the status of a feature, based on the available evidence." [SO:ke]	\N	status	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]	SO	732953	SO:0000909	SO:0000732	supported_by_EST_or_cDNA	SO:0000905
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	732954	SO:0000910	SO:0000905	orphan	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]	SO	732955	SO:0000911	SO:0000905	predicted_by_ab_initio_computation	SO:0000733
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	732956	SO:0000912	SO:0001078	asx_turn	SO:0001070
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A clone insert made from cDNA." [SO:xp]	SO	732957	SO:0000913	SO:0000151	cloned_cDNA_insert	SO:0000695
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A clone insert made from cDNA." [SO:xp]	SO	1165818	SO:0000913	SO:0000695	cloned_cDNA_insert	SO:0001409
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A clone insert made from genomic DNA." [SO:xp]	SO	732959	SO:0000914	SO:0000151	cloned_genomic_insert	SO:0000695
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A clone insert made from genomic DNA." [SO:xp]	SO	1165820	SO:0000914	SO:0000695	cloned_genomic_insert	SO:0001409
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A clone insert that is engineered." [SO:xp]	SO	732961	SO:0000915	SO:0000151	engineered_insert	SO:0000695
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A clone insert that is engineered." [SO:xp]	SO	1165822	SO:0000915	SO:0000695	engineered_insert	SO:0001409
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A clone insert that is engineered." [SO:xp]	SO	1679593	SO:0000915	SO:0000001	engineered_insert	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A clone insert that is engineered." [SO:xp]	SO	1259900	SO:0000915	SO:0001409	engineered_insert	SO:0000001
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA that is edited." [SO:xp]	SO	732965	SO:0000929	SO:0000233	edited_mRNA	SO:0000673
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA that is edited." [SO:xp]	SO	1165825	SO:0000929	SO:0000673	edited_mRNA	SO:0000831
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	732967	SO:0000930	SO:0000833	guide_RNA_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	732968	SO:0000930	SO:0000833	guide_RNA_region	SO:0001411
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	732969	SO:0000930	SO:0000655	guide_RNA_region	SO:0000233
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	732970	SO:0000931	SO:0000602	anchor_region	SO:0000655
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	732971	SO:0000931	SO:0000834	anchor_region	SO:0000833
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	732972	SO:0000932	SO:0000185	pre_edited_mRNA	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]	SO	732973	SO:0000934	SO:0000409	miRNA_target_site	SO:0001411
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	732974	SO:0000935	SO:0000836	edited_CDS	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	732975	SO:0000935	SO:0000836	edited_CDS	SO:0000834
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	732976	SO:0000936	SO:0000300	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000299
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	732977	SO:0000938	SO:0000300	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000299
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	732978	SO:0000939	SO:0000300	vertebrate_immune_system_gene_recombination_signal_feature	SO:0000299
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]	SO	732979	SO:0000941	SO:0000704	recombinationally_rearranged_vertebrate_immune_system_gene	SO:0001411
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	732980	SO:0000942	SO:0000342	attP_site	SO:0000299
3	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	732981	SO:0000942	SO:0001041	attP_site	SO:0001038
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	732982	SO:0000942	SO:0001041	attP_site	SO:0001235
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	732983	SO:0000943	SO:0000342	attB_site	SO:0000299
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	732984	SO:0000944	SO:0000342	attL_site	SO:0000299
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	732985	SO:0000945	SO:0000342	attR_site	SO:0000299
3	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	SO	732986	SO:0000946	SO:0000299	integration_excision_site	SO:0000669
3	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	SO	732987	SO:0000947	SO:0000299	resolution_site	SO:0000669
3	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	SO	732988	SO:0000948	SO:0000299	inversion_site	SO:0000669
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	732989	SO:0000949	SO:0000342	dif_site	SO:0000299
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	732990	SO:0000950	SO:0000342	attC_site	SO:0000299
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	732991	SO:0000950	SO:0001039	attC_site	SO:0001037
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	732992	SO:0000951	SO:0000673	eukaryotic_terminator	SO:0000831
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	732993	SO:0000951	SO:0001679	eukaryotic_terminator	SO:0005836
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An origin of vegetative replication in plasmids and phages." [SO:as]	SO	732994	SO:0000952	SO:0001235	oriV	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An origin of vegetative replication in plasmids and phages." [SO:as]	SO	1165856	SO:0000952	SO:0001411	oriV	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An origin of bacterial chromosome replication." [SO:as]	SO	732996	SO:0000953	SO:0001235	oriC	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An origin of bacterial chromosome replication." [SO:as]	SO	1165858	SO:0000953	SO:0001411	oriC	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	SO	732998	SO:0000954	SO:0001235	DNA_chromosome	SO:0001411
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	SO	732999	SO:0000955	SO:0000340	double_stranded_DNA_chromosome	SO:0001235
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	SO	733000	SO:0000956	SO:0000340	single_stranded_DNA_chromosome	SO:0001235
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	SO	733001	SO:0000957	SO:0000954	linear_double_stranded_DNA_chromosome	SO:0000340
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	SO	733002	SO:0000958	SO:0000954	circular_double_stranded_DNA_chromosome	SO:0000340
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	SO	733003	SO:0000959	SO:0000954	linear_single_stranded_DNA_chromosome	SO:0000340
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	733004	SO:0000960	SO:0000954	circular_single_stranded_DNA_chromosome	SO:0000340
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	SO	733005	SO:0000961	SO:0001235	RNA_chromosome	SO:0001411
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	SO	733006	SO:0000962	SO:0000340	single_stranded_RNA_chromosome	SO:0001235
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	SO	733007	SO:0000963	SO:0000961	linear_single_stranded_RNA_chromosome	SO:0000340
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	SO	733008	SO:0000964	SO:0000961	linear_double_stranded_RNA_chromosome	SO:0000340
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	SO	733009	SO:0000965	SO:0000340	double_stranded_RNA_chromosome	SO:0001235
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	733010	SO:0000966	SO:0000961	circular_single_stranded_RNA_chromosome	SO:0000340
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	\N	sequence	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	SO	733011	SO:0000967	SO:0000961	circular_double_stranded_RNA_chromosome	SO:0000340
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	733012	SO:0000973	SO:0000182	insertion_sequence	SO:0000101
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"" []	SO	733013	SO:0000975	SO:0000088	minicircle_gene	SO:0000704
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733014	SO:0000975	SO:0001235	minicircle_gene	SO:0001411
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	733015	SO:0000977	SO:0000673	anchor_binding_site	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640620	SO:0000977	SO:0001411	anchor_binding_site	SO:0000001
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	733017	SO:0000978	SO:0000602	template_region	SO:0000655
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	733018	SO:0000978	SO:0000834	template_region	SO:0000833
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A non-protein_coding gene that encodes a guide_RNA." [SO:ma]	SO	733019	SO:0000979	SO:0000401	gRNA_encoding	SO:0000733
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]	SO	733020	SO:0000980	SO:0001411	minicircle	SO:0000001
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	733021	SO:0000981	SO:0000141	rho_dependent_bacterial_terminator	SO:0000673
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	733022	SO:0000981	SO:0000141	rho_dependent_bacterial_terminator	SO:0001679
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	733023	SO:0000981	SO:0000752	rho_dependent_bacterial_terminator	SO:0001679
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	733024	SO:0000982	SO:0000141	rho_independent_bacterial_terminator	SO:0000673
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	733025	SO:0000982	SO:0000141	rho_independent_bacterial_terminator	SO:0001679
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	733026	SO:0000982	SO:0000752	rho_independent_bacterial_terminator	SO:0001679
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733027	SO:0000984	SO:0000733	single	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733028	SO:0000985	SO:0000733	double	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]	SO	733029	SO:0000987	SO:0000443	linear	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]	SO	733030	SO:0000988	SO:0000443	circular	SO:0000400
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	733031	SO:0000989	SO:0000233	class_II_RNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	733032	SO:0000990	SO:0000233	class_I_RNA	SO:0000673
3	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"" []	SO	733033	SO:0000991	SO:0000348	genomic_DNA	SO:0000443
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	SOFA	sequence	"" []	SO	733034	SO:0000992	SO:0000753	BAC_cloned_genomic_insert	SO:0000151
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"" []	SO	733035	SO:0000992	SO:0000753	BAC_cloned_genomic_insert	SO:0000695
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733036	SO:0000993	SO:0000733	consensus	SO:0000400
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	733038	SO:0000995	SO:0000233	consensus_mRNA	SO:0000673
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441461	SO:0000995	SO:0000001	consensus_mRNA	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	733040	SO:0000995	SO:0001410	consensus_mRNA	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	733041	SO:0000996	SO:0001411	predicted_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733042	SO:0000997	SO:0000704	gene_fragment	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165896	SO:0000997	SO:0001411	gene_fragment	SO:0000001
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	733044	SO:0000998	SO:0000162	recursive_splice_site	SO:0000835
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	1165901	SO:0000999	SO:0000143	BAC_end	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	733046	SO:0000999	SO:0000149	BAC_end	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	733047	SO:0000999	SO:0000149	BAC_end	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	733048	SO:0000999	SO:0000149	BAC_end	SO:0000353
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	733049	SO:0000999	SO:0000440	BAC_end	SO:0000151
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	733050	SO:0000999	SO:0000440	BAC_end	SO:0001235
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	733051	SO:0001000	SO:0000252	rRNA_16S	SO:0000655
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	733052	SO:0001001	SO:0000252	rRNA_23S	SO:0000655
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SOFA	ncRNA	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	733053	SO:0001002	SO:0000252	rRNA_25S	SO:0000655
3	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	733054	SO:0001003	SO:0000186	solo_LTR	SO:0000180
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	733055	SO:0001003	SO:0000657	solo_LTR	SO:0001411
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733056	SO:0001004	SO:0000733	low_complexity	SO:0000400
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	SO	733058	SO:0001006	SO:0001039	prophage	SO:0001037
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	SO	733059	SO:0001007	SO:0001039	cryptic_prophage	SO:0001037
3	"A folded sequence." [SO:ke]	\N	sequence_secondary_structure	\N	\N	sequence	"A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]	SO	733060	SO:0001008	SO:0000122	tetraloop	SO:0000002
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	SO	733061	SO:0001009	SO:0000696	DNA_constraint_sequence	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]	SO	733062	SO:0001010	SO:0000002	i_motif	SO:0001411
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]	SO	733063	SO:0001011	SO:0000696	PNA_oligo	SO:0000695
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A DNA sequence with catalytic activity." [SO:cb]	SO	733064	SO:0001012	SO:0000695	DNAzyme	SO:0001409
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	SO	733065	SO:0001013	SO:1000002	MNP	SO:0001059
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	SO	733066	SO:0001013	SO:1000002	MNP	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	762581	SO:0001014	SO:0000185	intron_domain	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	762582	SO:0001014	SO:0000833	intron_domain	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	762583	SO:0001014	SO:0000833	intron_domain	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]	SO	733072	SO:0001015	SO:0000002	wobble_base_pair	SO:0001411
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	1165931	SO:0001016	SO:0000188	internal_guide_sequence	SO:0000835
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	1259909	SO:0001016	SO:0000835	internal_guide_sequence	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	1259910	SO:0001016	SO:0000835	internal_guide_sequence	SO:0000833
3	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	intron	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	733076	SO:0001016	SO:0000588	internal_guide_sequence	SO:0000188
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke]	SO	733077	SO:0001017	SO:0001537	silent_mutation	SO:0001060
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]	SO	733078	SO:0001018	SO:0001411	epitope	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733079	SO:0001021	SO:0001235	chromosome_breakpoint	SO:0001411
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	733080	SO:0001022	SO:0000340	inversion_breakpoint	SO:0001235
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	733081	SO:0001022	SO:0000699	inversion_breakpoint	SO:0000110
3	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]	SO	733082	SO:0001025	SO:0001507	polymorphic_sequence_variant	SO:0001260
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]	SO	733083	SO:0001030	SO:0000733	forward	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke]	SO	733084	SO:0001031	SO:0000733	reverse	SO:0000400
3	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	733085	SO:0001032	SO:0000736	mitochondrial_DNA	SO:0000735
3	"" []	\N	organelle_sequence	\N	\N	sequence	"" []	SO	733086	SO:0001033	SO:0000740	chloroplast_DNA	SO:0000736
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	733087	SO:0001034	SO:0000188	mirtron	SO:0000835
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	1165937	SO:0001034	SO:0000835	mirtron	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	1165938	SO:0001034	SO:0000835	mirtron	SO:0000833
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	SO	733090	SO:0001035	SO:0000233	piRNA	SO:0000673
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	733091	SO:0001036	SO:0000655	arginyl_tRNA	SO:0000233
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An MGE that is not integrated into the host chromosome." [SO:ke]	SO	1165944	SO:0001038	SO:0000001	extrachromosomal_mobile_genetic_element	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An MGE that is not integrated into the host chromosome." [SO:ke]	SO	733094	SO:0001038	SO:0001411	extrachromosomal_mobile_genetic_element	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An MGE that is integrated into the host chromosome." [SO:ke]	SO	1165945	SO:0001039	SO:0000001	integrated_mobile_genetic_element	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An MGE that is integrated into the host chromosome." [SO:ke]	SO	733096	SO:0001039	SO:0001411	integrated_mobile_genetic_element	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid sequence that is integrated within the host chromosome." [SO:ke]	SO	733097	SO:0001040	SO:0001037	integrated_plasmid	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A plasmid sequence that is integrated within the host chromosome." [SO:ke]	SO	733098	SO:0001040	SO:0001037	integrated_plasmid	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	733099	SO:0001041	SO:0001037	viral_sequence	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	733100	SO:0001041	SO:0001037	viral_sequence	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	1165949	SO:0001041	SO:0001411	viral_sequence	SO:0000001
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	733102	SO:0001042	SO:0001038	phage_sequence	SO:0001037
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	733103	SO:0001042	SO:0001235	phage_sequence	SO:0001411
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	733104	SO:0001043	SO:0000342	attCtn_site	SO:0000299
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	733105	SO:0001043	SO:0000182	attCtn_site	SO:0000101
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]	SO	733106	SO:0001044	SO:0000336	nuclear_mt_pseudogene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]	SO	733107	SO:0001045	SO:0001037	cointegrated_plasmid	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]	SO	733108	SO:0001045	SO:0001037	cointegrated_plasmid	SO:0001411
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	733109	SO:0001046	SO:0000342	IRLinv_site	SO:0000299
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	733110	SO:0001047	SO:0000342	IRRinv_site	SO:0000299
3	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A region located within an inversion site." [SO:ke]	SO	733111	SO:0001048	SO:0000299	inversion_site_part	SO:0000669
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	SO	733112	SO:0001049	SO:0001039	defective_conjugative_transposon	SO:0001037
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	733113	SO:0001050	SO:0001412	repeat_fragment	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	733114	SO:0001050	SO:0000657	repeat_fragment	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	733115	SO:0001054	SO:0001412	transposon_fragment	SO:0000001
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	733116	SO:0001054	SO:0000101	transposon_fragment	SO:0001039
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SO	733117	SO:0001055	SO:0005836	transcriptional_cis_regulatory_region	SO:0000831
3	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A regulatory_region that modulates splicing." [SO:ke]	SO	733118	SO:0001056	SO:0005836	splicing_regulatory_region	SO:0000831
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	SO	733119	SO:0001058	SO:0001679	promoter_targeting_sequence	SO:0005836
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	1259920	SO:0001061	SO:0000839	propeptide_cleavage_site	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	1259921	SO:0001061	SO:0000839	propeptide_cleavage_site	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	762586	SO:0001061	SO:0001063	propeptide_cleavage_site	SO:0000839
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	1165974	SO:0001062	SO:0000839	propeptide	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	1165975	SO:0001062	SO:0000839	propeptide	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	733127	SO:0001062	SO:0001063	propeptide	SO:0000839
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	SOFA	sequence	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	SO	733128	SO:0001063	SO:0000104	immature_peptide_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens,SOFA	region	SOFA	SOFA	sequence	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	SO	1165976	SO:0001063	SO:0001411	immature_peptide_region	SO:0000001
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	1165980	SO:0001064	SO:0000839	active_peptide	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	1165981	SO:0001064	SO:0000839	active_peptide	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	733132	SO:0001064	SO:0001063	active_peptide	SO:0000839
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]	SO	733133	SO:0001066	SO:0000104	compositionally_biased_region_of_peptide	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]	SO	1165982	SO:0001066	SO:0001411	compositionally_biased_region_of_peptide	SO:0000001
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	SO	733135	SO:0001067	SO:0000839	polypeptide_motif	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	SO	733136	SO:0001067	SO:0000839	polypeptide_motif	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	SO	733137	SO:0001068	SO:0000839	polypeptide_repeat	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	SO	733138	SO:0001068	SO:0000839	polypeptide_repeat	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	SO	733139	SO:0001070	SO:0000104	polypeptide_structural_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	SO	1165988	SO:0001070	SO:0001411	polypeptide_structural_region	SO:0000001
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	SO	733141	SO:0001071	SO:0000839	membrane_structure	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	SO	733142	SO:0001071	SO:0000839	membrane_structure	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	762587	SO:0001072	SO:0000839	extramembrane_polypeptide_region	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	762588	SO:0001072	SO:0000839	extramembrane_polypeptide_region	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	1165996	SO:0001073	SO:0001070	cytoplasmic_polypeptide_region	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	733147	SO:0001073	SO:0001071	cytoplasmic_polypeptide_region	SO:0001070
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	1165999	SO:0001074	SO:0001070	non_cytoplasmic_polypeptide_region	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	733149	SO:0001074	SO:0001071	non_cytoplasmic_polypeptide_region	SO:0001070
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	762589	SO:0001075	SO:0000839	intramembrane_polypeptide_region	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	762590	SO:0001075	SO:0000839	intramembrane_polypeptide_region	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	1166004	SO:0001076	SO:0001070	membrane_peptide_loop	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	733154	SO:0001076	SO:0001071	membrane_peptide_loop	SO:0001070
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	1166007	SO:0001077	SO:0001070	transmembrane_polypeptide_region	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	733156	SO:0001077	SO:0001071	transmembrane_polypeptide_region	SO:0001070
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	SO	733157	SO:0001078	SO:0000839	polypeptide_secondary_structure	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	SO	733158	SO:0001078	SO:0000839	polypeptide_secondary_structure	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	SO	733159	SO:0001079	SO:0000839	polypeptide_structural_motif	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	SO	733160	SO:0001079	SO:0000839	polypeptide_structural_motif	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	733161	SO:0001080	SO:0001070	coiled_coil	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	733162	SO:0001081	SO:0001070	helix_turn_helix	SO:0000839
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	SO	733163	SO:0001082	SO:0001410	polypeptide_sequencing_information	SO:0000001
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	biosapiens	experimental_feature	SOFA	SOFA	sequence	"Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]	SO	733164	SO:0001083	SO:0000700	non_adjacent_residues	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	biosapiens	experimental_feature	SOFA	SOFA	sequence	"The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]	SO	733165	SO:0001084	SO:0000700	non_terminal_residue	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	biosapiens	experimental_feature	SOFA	SOFA	sequence	"Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]	SO	733166	SO:0001085	SO:0000700	sequence_conflict	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	biosapiens	experimental_feature	SOFA	SOFA	sequence	"Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]	SO	733167	SO:0001086	SO:0000700	sequence_uncertainty	SO:0001410
3	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	733168	SO:0001089	SO:0001067	post_translationally_modified_region	SO:0100021
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	733169	SO:0001092	SO:0000409	polypeptide_metal_contact	SO:0001411
3	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	733170	SO:0001092	SO:0100001	polypeptide_metal_contact	SO:0001067
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	733171	SO:0001093	SO:0000409	protein_protein_contact	SO:0001411
3	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	733172	SO:0001093	SO:0100001	protein_protein_contact	SO:0001067
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	733173	SO:0001094	SO:0001656	polypeptide_calcium_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	733174	SO:0001094	SO:0100002	polypeptide_calcium_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	733175	SO:0001095	SO:0001656	polypeptide_cobalt_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	733176	SO:0001095	SO:0100002	polypeptide_cobalt_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	733177	SO:0001096	SO:0001656	polypeptide_copper_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	733178	SO:0001096	SO:0100002	polypeptide_copper_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	733179	SO:0001097	SO:0001656	polypeptide_iron_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	733180	SO:0001097	SO:0100002	polypeptide_iron_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	733181	SO:0001098	SO:0001656	polypeptide_magnesium_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	733182	SO:0001098	SO:0100002	polypeptide_magnesium_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	733183	SO:0001099	SO:0001656	polypeptide_manganese_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	733184	SO:0001099	SO:0100002	polypeptide_manganese_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	733185	SO:0001100	SO:0001656	polypeptide_molybdenum_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	733186	SO:0001100	SO:0100002	polypeptide_molybdenum_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	733187	SO:0001101	SO:0001656	polypeptide_nickel_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	733188	SO:0001101	SO:0100002	polypeptide_nickel_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	733189	SO:0001102	SO:0001656	polypeptide_tungsten_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	733190	SO:0001102	SO:0100002	polypeptide_tungsten_ion_contact_site	SO:0100001
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	733191	SO:0001103	SO:0001656	polypeptide_zinc_ion_contact_site	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	biosapiens	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	733192	SO:0001103	SO:0100002	polypeptide_zinc_ion_contact_site	SO:0100001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	2441505	SO:0001104	SO:0000104	catalytic_residue	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	2452729	SO:0001104	SO:0001411	catalytic_residue	SO:0000001
3	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	733195	SO:0001104	SO:0100001	catalytic_residue	SO:0001067
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	733196	SO:0001105	SO:0000409	polypeptide_ligand_contact	SO:0001411
3	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	733197	SO:0001105	SO:0100001	polypeptide_ligand_contact	SO:0001067
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733198	SO:0001106	SO:0001070	asx_motif	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733199	SO:0001107	SO:0001070	beta_bulge	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733200	SO:0001108	SO:0001070	beta_bulge_loop	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733201	SO:0001109	SO:0001078	beta_bulge_loop_five	SO:0001070
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733202	SO:0001110	SO:0001078	beta_bulge_loop_six	SO:0001070
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	733203	SO:0001111	SO:0001070	beta_strand	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	733204	SO:0001112	SO:0001078	antiparallel_beta_strand	SO:0001070
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	733205	SO:0001113	SO:0001078	parallel_beta_strand	SO:0001070
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	733206	SO:0001114	SO:0001070	peptide_helix	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	733207	SO:0001115	SO:0001078	left_handed_peptide_helix	SO:0001070
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	733208	SO:0001116	SO:0001078	right_handed_peptide_helix	SO:0001070
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	733209	SO:0001117	SO:0001114	alpha_helix	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	733210	SO:0001118	SO:0001114	pi_helix	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	733211	SO:0001119	SO:0001114	three_ten_helix	SO:0001078
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733212	SO:0001120	SO:0001070	polypeptide_nest_motif	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733213	SO:0001121	SO:0001078	polypeptide_nest_left_right_motif	SO:0001070
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733214	SO:0001122	SO:0001078	polypeptide_nest_right_left_motif	SO:0001070
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733215	SO:0001123	SO:0001070	schellmann_loop	SO:0000839
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733216	SO:0001124	SO:0001078	schellmann_loop_seven	SO:0001070
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733217	SO:0001125	SO:0001078	schellmann_loop_six	SO:0001070
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733218	SO:0001126	SO:0001070	serine_threonine_motif	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733219	SO:0001127	SO:0001070	serine_threonine_staple_motif	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	733220	SO:0001128	SO:0001070	polypeptide_turn_motif	SO:0000839
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733221	SO:0001129	SO:0001128	asx_turn_left_handed_type_one	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733222	SO:0001130	SO:0001128	asx_turn_left_handed_type_two	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733223	SO:0001131	SO:0001128	asx_turn_right_handed_type_two	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733224	SO:0001132	SO:0001128	asx_turn_right_handed_type_one	SO:0001078
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733225	SO:0001133	SO:0001078	beta_turn	SO:0001070
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733226	SO:0001134	SO:0001128	beta_turn_left_handed_type_one	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733227	SO:0001135	SO:0001128	beta_turn_left_handed_type_two	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733228	SO:0001136	SO:0001128	beta_turn_right_handed_type_one	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733229	SO:0001137	SO:0001128	beta_turn_right_handed_type_two	SO:0001078
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733230	SO:0001138	SO:0001078	gamma_turn	SO:0001070
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733231	SO:0001139	SO:0001128	gamma_turn_classic	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733232	SO:0001140	SO:0001128	gamma_turn_inverse	SO:0001078
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733233	SO:0001141	SO:0001078	serine_threonine_turn	SO:0001070
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733234	SO:0001142	SO:0001128	st_turn_left_handed_type_one	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733235	SO:0001143	SO:0001128	st_turn_left_handed_type_two	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733236	SO:0001144	SO:0001128	st_turn_right_handed_type_one	SO:0001078
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	733237	SO:0001145	SO:0001128	st_turn_right_handed_type_two	SO:0001078
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	SO	733238	SO:0001146	SO:0000104	polypeptide_variation_site	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	SO	1166101	SO:0001146	SO:0001411	polypeptide_variation_site	SO:0000001
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	SO	733240	SO:0001147	SO:0000839	natural_variant_site	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	SO	733241	SO:0001147	SO:0000839	natural_variant_site	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	SO	733242	SO:0001148	SO:0000839	mutated_variant_site	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	SO	733243	SO:0001148	SO:0000839	mutated_variant_site	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	SO	733244	SO:0001149	SO:0000839	alternate_sequence_site	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	SO	733245	SO:0001149	SO:0000839	alternate_sequence_site	SO:0001411
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	733246	SO:0001150	SO:0001128	beta_turn_type_six	SO:0001078
3	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	733247	SO:0001151	SO:0001133	beta_turn_type_six_a	SO:0001128
3	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"" []	SO	733248	SO:0001152	SO:0001150	beta_turn_type_six_a_one	SO:0001133
3	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	biosapiens	beta_turn	biosapiens	biosapiens	sequence	"" []	SO	733249	SO:0001153	SO:0001150	beta_turn_type_six_a_two	SO:0001133
3	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	733250	SO:0001154	SO:0001133	beta_turn_type_six_b	SO:0001128
3	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	733251	SO:0001155	SO:0001128	beta_turn_type_eight	SO:0001078
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	733252	SO:0001156	SO:0000714	DRE_motif	SO:0001683
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	733253	SO:0001156	SO:0001203	DRE_motif	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	SO	733254	SO:0001157	SO:0000713	DMv4_motif	SO:0000714
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	733255	SO:0001158	SO:0000714	E_box_motif	SO:0001683
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	733256	SO:0001158	SO:0001203	E_box_motif	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	733257	SO:0001159	SO:0000713	DMv5_motif	SO:0000714
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	733258	SO:0001159	SO:0001203	DMv5_motif	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	733259	SO:0001160	SO:0000713	DMv3_motif	SO:0000714
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	733260	SO:0001160	SO:0001203	DMv3_motif	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	733261	SO:0001161	SO:0000713	DMv2_motif	SO:0000714
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	733262	SO:0001161	SO:0001203	DMv2_motif	SO:0000167
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	733263	SO:0001162	SO:0001659	MTE	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	733264	SO:0001162	SO:0000170	MTE	SO:0001203
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	733265	SO:0001163	SO:0000714	INR1_motif	SO:0001683
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	733266	SO:0001163	SO:0001203	INR1_motif	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	733267	SO:0001164	SO:0000713	DPE1_motif	SO:0000714
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	733268	SO:0001164	SO:0001203	DPE1_motif	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	733269	SO:0001165	SO:0000713	DMv1_motif	SO:0000714
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	733270	SO:0001165	SO:0001203	DMv1_motif	SO:0000167
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	733271	SO:0001166	SO:0000714	GAGA_motif	SO:0001683
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	733272	SO:0001166	SO:0001203	GAGA_motif	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	733273	SO:0001167	SO:0000713	NDM2_motif	SO:0000714
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	733274	SO:0001167	SO:0001203	NDM2_motif	SO:0000167
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	733275	SO:0001168	SO:0000713	NDM3_motif	SO:0000714
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	733276	SO:0001168	SO:0001203	NDM3_motif	SO:0000167
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	733277	SO:0001169	SO:0001038	ds_RNA_viral_sequence	SO:0001037
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	733278	SO:0001169	SO:0001235	ds_RNA_viral_sequence	SO:0001411
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	733279	SO:0001170	SO:0000182	polinton	SO:0000101
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	733280	SO:0001171	SO:0000252	rRNA_21S	SO:0000655
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	733281	SO:0001172	SO:0000833	tRNA_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	733282	SO:0001172	SO:0000833	tRNA_region	SO:0001411
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	733283	SO:0001172	SO:0000655	tRNA_region	SO:0000233
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	733284	SO:0001173	SO:0000253	anticodon_loop	SO:0000655
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	733285	SO:0001173	SO:0000834	anticodon_loop	SO:0000833
4	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	762591	SO:0001174	SO:0000253	anticodon	SO:0000655
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	762592	SO:0001174	SO:0000834	anticodon	SO:0000833
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	733290	SO:0001175	SO:0000253	CCA_tail	SO:0000655
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	733291	SO:0001175	SO:0000834	CCA_tail	SO:0000833
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	733292	SO:0001176	SO:0000253	DHU_loop	SO:0000655
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	733293	SO:0001176	SO:0000834	DHU_loop	SO:0000833
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	733294	SO:0001177	SO:0000253	T_loop	SO:0000655
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	733295	SO:0001177	SO:0000834	T_loop	SO:0000833
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	733296	SO:0001178	SO:0000483	pyrrolysine_tRNA_primary_transcript	SO:0000185
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	733297	SO:0001179	SO:0000275	U3_snoRNA	SO:0000655
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	1166167	SO:0001180	SO:0000836	AU_rich_element	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	1166168	SO:0001180	SO:0000836	AU_rich_element	SO:0000834
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	733300	SO:0001180	SO:0000203	AU_rich_element	SO:0000836
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	1166171	SO:0001181	SO:0000836	Bruno_response_element	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	1166172	SO:0001181	SO:0000836	Bruno_response_element	SO:0000834
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	733303	SO:0001181	SO:0000203	Bruno_response_element	SO:0000836
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	733304	SO:0001182	SO:0000836	iron_responsive_element	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	733305	SO:0001182	SO:0000836	iron_responsive_element	SO:0000834
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]	SO	733306	SO:0001183	SO:0000443	morpholino_backbone	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]	SO	733307	SO:0001184	SO:0000443	PNA	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]	SO	733308	SO:0001186	SO:0000733	ribozymic	SO:0000400
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	733309	SO:0001187	SO:0000275	pseudouridylation_guide_snoRNA	SO:0000655
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]	SO	733310	SO:0001188	SO:0000443	LNA	SO:0000400
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An oligo composed of LNA residues." [RSC:cb]	SO	733311	SO:0001189	SO:0000696	LNA_oligo	SO:0000695
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]	SO	733312	SO:0001190	SO:0000443	TNA	SO:0000400
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An oligo composed of TNA residues." [RSC:cb]	SO	733313	SO:0001191	SO:0000696	TNA_oligo	SO:0000695
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]	SO	733314	SO:0001192	SO:0000443	GNA	SO:0000400
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An oligo composed of GNA residues." [RSC:cb]	SO	733315	SO:0001193	SO:0000696	GNA_oligo	SO:0000695
3	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]	SO	733316	SO:0001194	SO:0000348	R_GNA	SO:0000443
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"An oligo composed of (R)-GNA residues." [RSC:cb]	SO	733317	SO:0001195	SO:0001247	R_GNA_oligo	SO:0000696
3	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]	SO	733318	SO:0001196	SO:0000348	S_GNA	SO:0000443
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	\N	sequence	"An oligo composed of (S)-GNA residues." [RSC:cb]	SO	733319	SO:0001197	SO:0001247	S_GNA_oligo	SO:0000696
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	733320	SO:0001198	SO:0001038	ds_DNA_viral_sequence	SO:0001037
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	733321	SO:0001198	SO:0001235	ds_DNA_viral_sequence	SO:0001411
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	733322	SO:0001199	SO:0001038	ss_RNA_viral_sequence	SO:0001037
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	733323	SO:0001199	SO:0001235	ss_RNA_viral_sequence	SO:0001411
3	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	733324	SO:0001200	SO:0001041	negative_sense_ssRNA_viral_sequence	SO:0001038
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	733325	SO:0001200	SO:0001041	negative_sense_ssRNA_viral_sequence	SO:0001235
3	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	733326	SO:0001201	SO:0001041	positive_sense_ssRNA_viral_sequence	SO:0001038
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	733327	SO:0001201	SO:0001041	positive_sense_ssRNA_viral_sequence	SO:0001235
3	"An MGE that is not integrated into the host chromosome." [SO:ke]	\N	extrachromosomal_mobile_genetic_element	\N	\N	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	733328	SO:0001202	SO:0001041	ambisense_ssRNA_viral_sequence	SO:0001038
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	733329	SO:0001202	SO:0001041	ambisense_ssRNA_viral_sequence	SO:0001235
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	733330	SO:0001203	SO:0001055	RNA_polymerase_promoter	SO:0001679
3	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	733331	SO:0001204	SO:0000167	Phage_RNA_Polymerase_Promoter	SO:0001055
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	733332	SO:0001205	SO:0001203	SP6_RNA_Polymerase_Promoter	SO:0000167
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	733333	SO:0001206	SO:0001203	T3_RNA_Polymerase_Promoter	SO:0000167
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	733334	SO:0001207	SO:0001203	T7_RNA_Polymerase_Promoter	SO:0000167
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	733335	SO:0001208	SO:0000324	five_prime_EST	SO:0000696
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	733336	SO:0001209	SO:0000324	three_prime_EST	SO:0000696
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	733337	SO:0001210	SO:0000234	translational_frameshift	SO:0000233
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	733338	SO:0001210	SO:0000834	translational_frameshift	SO:0000833
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	733339	SO:0001211	SO:0000836	plus_1_translational_frameshift	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	733340	SO:0001211	SO:0000836	plus_1_translational_frameshift	SO:0000834
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	733341	SO:0001212	SO:0000836	plus_2_translational_frameshift	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	733342	SO:0001212	SO:0000836	plus_2_translational_frameshift	SO:0000834
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	733343	SO:0001213	SO:0000188	group_III_intron	SO:0000835
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	733344	SO:0001214	SO:0000147	noncoding_region_of_exon	SO:0000833
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	1166211	SO:0001214	SO:0000833	noncoding_region_of_exon	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	1166212	SO:0001214	SO:0000833	noncoding_region_of_exon	SO:0001411
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	733347	SO:0001215	SO:0000147	coding_region_of_exon	SO:0000833
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	1166215	SO:0001215	SO:0000833	coding_region_of_exon	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	1166216	SO:0001215	SO:0000833	coding_region_of_exon	SO:0001411
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	733350	SO:0001216	SO:0000835	endonuclease_spliced_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	733351	SO:0001216	SO:0000835	endonuclease_spliced_intron	SO:0000833
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	733352	SO:0001217	SO:0001411	protein_coding_gene	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]	SO	733353	SO:0001218	SO:0001059	transgenic_insertion	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]	SO	733354	SO:0001218	SO:0001411	transgenic_insertion	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	733355	SO:0001219	SO:0001411	retrogene	SO:0000001
3	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	SO	733356	SO:0001220	SO:0000126	silenced_by_RNA_interference	SO:0000123
3	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	SO	733357	SO:0001221	SO:0000126	silenced_by_histone_modification	SO:0000123
3	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	733358	SO:0001222	SO:0000893	silenced_by_histone_methylation	SO:0000126
3	"A repressor molecule is required for transcription to stop." [SO:ke]	\N	transcriptionally_repressed	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	733359	SO:0001223	SO:0000893	silenced_by_histone_deacetylation	SO:0000126
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is silenced by RNA interference." [SO:xp]	SO	733360	SO:0001224	SO:0000704	gene_silenced_by_RNA_interference	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is silenced by histone modification." [SO:xp]	SO	733361	SO:0001225	SO:0000704	gene_silenced_by_histone_modification	SO:0001411
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced by histone methylation." [SO:xp]	SO	733362	SO:0001226	SO:0000127	gene_silenced_by_histone_methylation	SO:0000704
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene that is silenced by histone deacetylation." [SO:xp]	SO	733363	SO:0001227	SO:0000127	gene_silenced_by_histone_deacetylation	SO:0000704
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]	SO	733364	SO:0001228	SO:0000250	dihydrouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]	SO	733365	SO:0001229	SO:0000250	pseudouridine	SO:0001236
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	SO	733366	SO:0001230	SO:0001236	inosine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]	SO	733367	SO:0001231	SO:0001236	seven_methylguanine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]	SO	733368	SO:0001232	SO:0001236	ribothymidine	SO:0001411
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	SO	733369	SO:0001233	SO:0001230	methylinosine	SO:0000250
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SO	733370	SO:0001235	SO:0000001	replicon	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	SO	733371	SO:0001236	SO:0000001	base	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]	SO	762593	SO:0001237	SO:0000001	amino_acid	SO:0000110
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	733374	SO:0001238	SO:0000835	major_TSS	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	733375	SO:0001238	SO:0000835	major_TSS	SO:0000833
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	733376	SO:0001239	SO:0000835	minor_TSS	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	733377	SO:0001239	SO:0000835	minor_TSS	SO:0000833
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]	SO	733378	SO:0001240	SO:0000704	TSS_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]	SO	1166245	SO:0001240	SO:0001411	TSS_region	SO:0000001
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733380	SO:0001241	SO:0000733	encodes_alternate_transcription_start_sites	SO:0000400
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	733381	SO:0001243	SO:0000185	miRNA_primary_transcript_region	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	733382	SO:0001243	SO:0000833	miRNA_primary_transcript_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	733383	SO:0001243	SO:0000833	miRNA_primary_transcript_region	SO:0001411
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	733384	SO:0001244	SO:0000835	pre_miRNA	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	733385	SO:0001244	SO:0000835	pre_miRNA	SO:0000833
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	733386	SO:0001244	SO:0000483	pre_miRNA	SO:0000185
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	762594	SO:0001245	SO:0000835	miRNA_stem	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	762595	SO:0001245	SO:0000835	miRNA_stem	SO:0000833
3	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	733389	SO:0001245	SO:0000647	miRNA_stem	SO:0000483
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	762596	SO:0001246	SO:0000835	miRNA_loop	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	762597	SO:0001246	SO:0000835	miRNA_loop	SO:0000833
3	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	\N	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	733393	SO:0001246	SO:0000647	miRNA_loop	SO:0000483
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An oligo composed of synthetic nucleotides." [SO:ke]	SO	733395	SO:0001247	SO:0000695	synthetic_oligo	SO:0001409
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	SO	733396	SO:0001248	SO:0000001	assembly	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	SO	733397	SO:0001249	SO:0001410	fragment_assembly	SO:0000001
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]	SO	733398	SO:0001250	SO:0001248	fingerprint_map	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"An STS map is a physical map organized by the unique STS landmarks." [SO:ke]	SO	733399	SO:0001251	SO:0001248	STS_map	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A radiation hybrid map is a physical map." [SO:ke]	SO	733400	SO:0001252	SO:0001248	RH_map	SO:0001410
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]	SO	733401	SO:0001253	SO:0001410	sonicate_fragment	SO:0000001
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	733402	SO:0001254	SO:0000240	polyploid	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	733403	SO:0001254	SO:0000240	polyploid	SO:0001524
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	733404	SO:0001255	SO:1000182	autopolyploid	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	733405	SO:0001256	SO:1000182	allopolyploid	SO:0000240
3	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	SOFA	sequence	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	SO	733406	SO:0001257	SO:0001654	homing_endonuclease_binding_site	SO:0000410
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	733407	SO:0001258	SO:0000714	octamer_motif	SO:0001683
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	733408	SO:0001258	SO:0001203	octamer_motif	SO:0000167
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A chromosome originating in an apicoplast." [SO:xp]	SO	733409	SO:0001259	SO:0001235	apicoplast_chromosome	SO:0001411
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]	SO	733410	SO:0001261	SO:0000700	overlapping_feature_set	SO:0001410
3	"A comment about the sequence." [SO:ke]	\N	remark	SOFA	SOFA	sequence	"A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]	SO	733411	SO:0001262	SO:0000703	overlapping_EST_set	SO:0000700
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	733412	SO:0001263	SO:0001411	ncRNA_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733413	SO:0001264	SO:0000704	gRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733414	SO:0001265	SO:0000704	miRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733415	SO:0001266	SO:0000704	scRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733416	SO:0001267	SO:0000704	snoRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733417	SO:0001268	SO:0000704	snRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733418	SO:0001269	SO:0000704	SRP_RNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733419	SO:0001270	SO:0000704	stRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733420	SO:0001271	SO:0000704	tmRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733421	SO:0001272	SO:0000704	tRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	SO	733422	SO:0001273	SO:0001236	modified_adenosine	SO:0001411
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	SO	733423	SO:0001274	SO:0000250	modified_inosine	SO:0001236
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	SO	733424	SO:0001275	SO:0001236	modified_cytidine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733425	SO:0001276	SO:0001236	modified_guanosine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733426	SO:0001277	SO:0001236	modified_uridine	SO:0001411
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	733427	SO:0001278	SO:0001230	one_methylinosine	SO:0000250
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	733428	SO:0001279	SO:0001230	one_two_prime_O_dimethylinosine	SO:0000250
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	733429	SO:0001280	SO:0001230	two_prime_O_methylinosine	SO:0000250
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733430	SO:0001281	SO:0000250	three_methylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733431	SO:0001282	SO:0000250	five_methylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733432	SO:0001283	SO:0000250	two_prime_O_methylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733433	SO:0001284	SO:0000250	two_thiocytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733434	SO:0001285	SO:0000250	N4_acetylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733435	SO:0001286	SO:0000250	five_formylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733436	SO:0001287	SO:0000250	five_two_prime_O_dimethylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733437	SO:0001288	SO:0000250	N4_acetyl_2_prime_O_methylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733438	SO:0001289	SO:0000250	lysidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733439	SO:0001290	SO:0000250	N4_methylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733440	SO:0001291	SO:0000250	N4_2_prime_O_dimethylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733441	SO:0001292	SO:0000250	five_hydroxymethylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733442	SO:0001293	SO:0000250	five_formyl_two_prime_O_methylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	733443	SO:0001294	SO:0000250	N4_N4_2_prime_O_trimethylcytidine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733444	SO:0001295	SO:0000250	one_methyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733445	SO:0001296	SO:0000250	two_methyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733446	SO:0001297	SO:0000250	N6_methyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733447	SO:0001298	SO:0000250	two_prime_O_methyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733448	SO:0001299	SO:0000250	two_methylthio_N6_methyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733449	SO:0001300	SO:0000250	N6_isopentenyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733450	SO:0001301	SO:0000250	two_methylthio_N6_isopentenyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733451	SO:0001302	SO:0000250	N6_cis_hydroxyisopentenyl_adenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733452	SO:0001303	SO:0000250	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733453	SO:0001304	SO:0000250	N6_glycinylcarbamoyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733454	SO:0001305	SO:0000250	N6_threonylcarbamoyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733455	SO:0001306	SO:0000250	two_methylthio_N6_threonyl_carbamoyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733456	SO:0001307	SO:0000250	N6_methyl_N6_threonylcarbamoyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733457	SO:0001308	SO:0000250	N6_hydroxynorvalylcarbamoyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733458	SO:0001309	SO:0000250	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733459	SO:0001310	SO:0000250	two_prime_O_ribosyladenosine_phosphate	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733460	SO:0001311	SO:0000250	N6_N6_dimethyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733461	SO:0001312	SO:0000250	N6_2_prime_O_dimethyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733462	SO:0001313	SO:0000250	N6_N6_2_prime_O_trimethyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733463	SO:0001314	SO:0000250	one_two_prime_O_dimethyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	733464	SO:0001315	SO:0000250	N6_acetyladenosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	SO	733465	SO:0001316	SO:0000250	seven_deazaguanosine	SO:0001236
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	733466	SO:0001317	SO:0001276	queuosine	SO:0000250
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	733467	SO:0001318	SO:0001276	epoxyqueuosine	SO:0000250
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	733468	SO:0001319	SO:0001276	galactosyl_queuosine	SO:0000250
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	733469	SO:0001320	SO:0001276	mannosyl_queuosine	SO:0000250
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	733470	SO:0001321	SO:0001276	seven_cyano_seven_deazaguanosine	SO:0000250
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	733471	SO:0001322	SO:0001276	seven_aminomethyl_seven_deazaguanosine	SO:0000250
3	"A post_transcriptionally modified base." [SO:ke]	\N	modified_RNA_base_feature	\N	\N	sequence	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	733472	SO:0001323	SO:0001276	archaeosine	SO:0000250
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733473	SO:0001324	SO:0000250	one_methylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733474	SO:0001325	SO:0000250	N2_methylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733475	SO:0001326	SO:0000250	seven_methylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733476	SO:0001327	SO:0000250	two_prime_O_methylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733477	SO:0001328	SO:0000250	N2_N2_dimethylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733478	SO:0001329	SO:0000250	N2_2_prime_O_dimethylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733479	SO:0001330	SO:0000250	N2_N2_2_prime_O_trimethylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733480	SO:0001331	SO:0000250	two_prime_O_ribosylguanosine_phosphate	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733481	SO:0001332	SO:0000250	wybutosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733482	SO:0001333	SO:0000250	peroxywybutosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733483	SO:0001334	SO:0000250	hydroxywybutosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733484	SO:0001335	SO:0000250	undermodified_hydroxywybutosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733485	SO:0001336	SO:0000250	wyosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733486	SO:0001337	SO:0000250	methylwyosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733487	SO:0001338	SO:0000250	N2_7_dimethylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733488	SO:0001339	SO:0000250	N2_N2_7_trimethylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733489	SO:0001340	SO:0000250	one_two_prime_O_dimethylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733490	SO:0001341	SO:0000250	four_demethylwyosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733491	SO:0001342	SO:0000250	isowyosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733492	SO:0001343	SO:0000250	N2_7_2prirme_O_trimethylguanosine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733493	SO:0001344	SO:0000250	five_methyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733494	SO:0001345	SO:0000250	two_prime_O_methyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733495	SO:0001346	SO:0000250	five_two_prime_O_dimethyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733496	SO:0001347	SO:0000250	one_methylpseudouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733497	SO:0001348	SO:0000250	two_prime_O_methylpseudouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733498	SO:0001349	SO:0000250	two_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733499	SO:0001350	SO:0000250	four_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733500	SO:0001351	SO:0000250	five_methyl_2_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733501	SO:0001352	SO:0000250	two_thio_two_prime_O_methyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733502	SO:0001353	SO:0000250	three_three_amino_three_carboxypropyl_uridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733503	SO:0001354	SO:0000250	five_hydroxyuridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733504	SO:0001355	SO:0000250	five_methoxyuridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733505	SO:0001356	SO:0000250	uridine_five_oxyacetic_acid	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733506	SO:0001357	SO:0000250	uridine_five_oxyacetic_acid_methyl_ester	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733507	SO:0001358	SO:0000250	five_carboxyhydroxymethyl_uridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733508	SO:0001359	SO:0000250	five_carboxyhydroxymethyl_uridine_methyl_ester	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733509	SO:0001360	SO:0000250	five_methoxycarbonylmethyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733510	SO:0001361	SO:0000250	five_methoxycarbonylmethyl_two_prime_O_methyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733511	SO:0001362	SO:0000250	five_methoxycarbonylmethyl_two_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733512	SO:0001363	SO:0000250	five_aminomethyl_two_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733513	SO:0001364	SO:0000250	five_methylaminomethyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733514	SO:0001365	SO:0000250	five_methylaminomethyl_two_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733515	SO:0001366	SO:0000250	five_methylaminomethyl_two_selenouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733516	SO:0001367	SO:0000250	five_carbamoylmethyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733517	SO:0001368	SO:0000250	five_carbamoylmethyl_two_prime_O_methyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733518	SO:0001369	SO:0000250	five_carboxymethylaminomethyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733519	SO:0001370	SO:0000250	five_carboxymethylaminomethyl_two_prime_O_methyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733520	SO:0001371	SO:0000250	five_carboxymethylaminomethyl_two_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733521	SO:0001372	SO:0000250	three_methyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733522	SO:0001373	SO:0000250	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733523	SO:0001374	SO:0000250	five_carboxymethyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733524	SO:0001375	SO:0000250	three_two_prime_O_dimethyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733525	SO:0001376	SO:0000250	five_methyldihydrouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733526	SO:0001377	SO:0000250	three_methylpseudouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733527	SO:0001378	SO:0000250	five_taurinomethyluridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733528	SO:0001379	SO:0000250	five_taurinomethyl_two_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733529	SO:0001380	SO:0000250	five_isopentenylaminomethyl_uridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733530	SO:0001381	SO:0000250	five_isopentenylaminomethyl_two_thiouridine	SO:0001236
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	733531	SO:0001382	SO:0000250	five_isopentenylaminomethyl_two_prime_O_methyluridine	SO:0001236
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]	SO	733532	SO:0001383	SO:0000410	histone_binding_site	SO:0000409
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"" []	SO	733533	SO:0001384	SO:0000836	CDS_fragment	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"" []	SO	733534	SO:0001384	SO:0000836	CDS_fragment	SO:0000834
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified amino acid feature." [SO:ke]	SO	733535	SO:0001385	SO:0000104	modified_amino_acid_feature	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified amino acid feature." [SO:ke]	SO	1166401	SO:0001385	SO:0001411	modified_amino_acid_feature	SO:0000001
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified glycine amino acid feature." [SO:ke]	SO	733537	SO:0001386	SO:0001237	modified_glycine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified glycine amino acid feature." [SO:ke]	SO	733538	SO:0001386	SO:0001237	modified_glycine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified alanine amino acid feature." [SO:ke]	SO	733539	SO:0001387	SO:0001237	modified_L_alanine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified alanine amino acid feature." [SO:ke]	SO	733540	SO:0001387	SO:0001237	modified_L_alanine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified asparagine amino acid feature." [SO:ke]	SO	733541	SO:0001388	SO:0001237	modified_L_asparagine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified asparagine amino acid feature." [SO:ke]	SO	733542	SO:0001388	SO:0001237	modified_L_asparagine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	SO	733543	SO:0001389	SO:0001237	modified_L_aspartic_acid	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	SO	733544	SO:0001389	SO:0001237	modified_L_aspartic_acid	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified cysteine amino acid feature." [SO:ke]	SO	733545	SO:0001390	SO:0001237	modified_L_cysteine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified cysteine amino acid feature." [SO:ke]	SO	733546	SO:0001390	SO:0001237	modified_L_cysteine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"" []	SO	733547	SO:0001391	SO:0001237	modified_L_glutamic_acid	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	733548	SO:0001391	SO:0001237	modified_L_glutamic_acid	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified threonine amino acid feature." [SO:ke]	SO	733549	SO:0001392	SO:0001237	modified_L_threonine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified threonine amino acid feature." [SO:ke]	SO	733550	SO:0001392	SO:0001237	modified_L_threonine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified tryptophan amino acid feature." [SO:ke]	SO	733551	SO:0001393	SO:0001237	modified_L_tryptophan	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified tryptophan amino acid feature." [SO:ke]	SO	733552	SO:0001393	SO:0001237	modified_L_tryptophan	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified glutamine amino acid feature." [SO:ke]	SO	733553	SO:0001394	SO:0001237	modified_L_glutamine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified glutamine amino acid feature." [SO:ke]	SO	733554	SO:0001394	SO:0001237	modified_L_glutamine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified methionine amino acid feature." [SO:ke]	SO	733555	SO:0001395	SO:0001237	modified_L_methionine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified methionine amino acid feature." [SO:ke]	SO	733556	SO:0001395	SO:0001237	modified_L_methionine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified isoleucine amino acid feature." [SO:ke]	SO	733557	SO:0001396	SO:0001237	modified_L_isoleucine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified isoleucine amino acid feature." [SO:ke]	SO	733558	SO:0001396	SO:0001237	modified_L_isoleucine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	SO	733559	SO:0001397	SO:0001237	modified_L_phenylalanine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	SO	733560	SO:0001397	SO:0001237	modified_L_phenylalanine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified histidine amino acid feature." [SO:ke]	SO	733561	SO:0001398	SO:0001237	modified_L_histidine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified histidine amino acid feature." [SO:ke]	SO	733562	SO:0001398	SO:0001237	modified_L_histidine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified serine amino acid feature." [SO:ke]	SO	733563	SO:0001399	SO:0001237	modified_L_serine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified serine amino acid feature." [SO:ke]	SO	733564	SO:0001399	SO:0001237	modified_L_serine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified lysine amino acid feature." [SO:ke]	SO	733565	SO:0001400	SO:0001237	modified_L_lysine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified lysine amino acid feature." [SO:ke]	SO	733566	SO:0001400	SO:0001237	modified_L_lysine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified leucine amino acid feature." [SO:ke]	SO	733567	SO:0001401	SO:0001237	modified_L_leucine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified leucine amino acid feature." [SO:ke]	SO	733568	SO:0001401	SO:0001237	modified_L_leucine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	SO	733569	SO:0001402	SO:0001237	modified_L_selenocysteine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	SO	733570	SO:0001402	SO:0001237	modified_L_selenocysteine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified valine amino acid feature." [SO:ke]	SO	733571	SO:0001403	SO:0001237	modified_L_valine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified valine amino acid feature." [SO:ke]	SO	733572	SO:0001403	SO:0001237	modified_L_valine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified proline amino acid feature." [SO:ke]	SO	733573	SO:0001404	SO:0001237	modified_L_proline	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified proline amino acid feature." [SO:ke]	SO	733574	SO:0001404	SO:0001237	modified_L_proline	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified tyrosine amino acid feature." [SO:ke]	SO	733575	SO:0001405	SO:0001237	modified_L_tyrosine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified tyrosine amino acid feature." [SO:ke]	SO	733576	SO:0001405	SO:0001237	modified_L_tyrosine	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	\N	sequence	"A post translationally modified arginine amino acid feature." [SO:ke]	SO	733577	SO:0001406	SO:0001237	modified_L_arginine	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A post translationally modified arginine amino acid feature." [SO:ke]	SO	733578	SO:0001406	SO:0001237	modified_L_arginine	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	1166447	SO:0001408	SO:0000839	cleaved_for_gpi_anchor_region	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	1166448	SO:0001408	SO:0000839	cleaved_for_gpi_anchor_region	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	733581	SO:0001408	SO:0001063	cleaved_for_gpi_anchor_region	SO:0000839
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	733582	SO:0001413	SO:0000340	translocation_breakpoint	SO:0001235
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	733583	SO:0001413	SO:0000699	translocation_breakpoint	SO:0000110
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	733584	SO:0001414	SO:0000340	insertion_breakpoint	SO:0001235
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	733585	SO:0001414	SO:0000699	insertion_breakpoint	SO:0000110
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	733586	SO:0001415	SO:0000340	deletion_breakpoint	SO:0001235
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	733587	SO:0001415	SO:0000699	deletion_breakpoint	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A flanking region located five prime of a specific region." [SO:chado]	SO	733588	SO:0001416	SO:0001412	five_prime_flanking_region	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A flanking region located three prime of a specific region." [SO:chado]	SO	733589	SO:0001417	SO:0001412	three_prime_flanking_region	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]	SO	733590	SO:0001418	SO:0000001	transcribed_fragment	SO:0000110
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	733591	SO:0001419	SO:0000835	cis_splice_site	SO:0000185
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	733592	SO:0001419	SO:0000835	cis_splice_site	SO:0000833
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	733593	SO:0001420	SO:0000835	trans_splice_site	SO:0000185
3	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	733594	SO:0001420	SO:0000835	trans_splice_site	SO:0000833
3	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	733595	SO:0001422	SO:0001067	conformational_switch	SO:0100021
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	1166462	SO:0001423	SO:0000143	dye_terminator_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	733597	SO:0001423	SO:0000149	dye_terminator_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	733598	SO:0001423	SO:0000149	dye_terminator_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	733599	SO:0001423	SO:0000149	dye_terminator_read	SO:0000353
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	1166467	SO:0001424	SO:0000143	pyrosequenced_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	733601	SO:0001424	SO:0000149	pyrosequenced_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	733602	SO:0001424	SO:0000149	pyrosequenced_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	733603	SO:0001424	SO:0000149	pyrosequenced_read	SO:0000353
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	1166472	SO:0001425	SO:0000143	ligation_based_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	733605	SO:0001425	SO:0000149	ligation_based_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	733606	SO:0001425	SO:0000149	ligation_based_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	733607	SO:0001425	SO:0000149	ligation_based_read	SO:0000353
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	1166477	SO:0001426	SO:0000143	polymerase_synthesis_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	733609	SO:0001426	SO:0000149	polymerase_synthesis_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	733610	SO:0001426	SO:0000149	polymerase_synthesis_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	733611	SO:0001426	SO:0000149	polymerase_synthesis_read	SO:0000353
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]	SO	733612	SO:0001427	SO:0005836	cis_regulatory_frameshift_element	SO:0000831
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequence assembly derived from expressed sequences." [SO:ke]	SO	733613	SO:0001428	SO:0001248	expressed_sequence_assembly	SO:0001410
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	SO	733614	SO:0001429	SO:0000409	DNA_binding_site	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]	SO	733615	SO:0001431	SO:0001411	cryptic_gene	SO:0000001
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]	SO	733616	SO:0001433	SO:0000151	three_prime_RACE_clone	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]	SO	733617	SO:0001434	SO:0000336	cassette_pseudogene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733618	SO:0001435	SO:0000104	alanine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166487	SO:0001435	SO:0001411	alanine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733620	SO:0001436	SO:0000104	valine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166489	SO:0001436	SO:0001411	valine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733622	SO:0001437	SO:0000104	leucine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166491	SO:0001437	SO:0001411	leucine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733624	SO:0001438	SO:0000104	isoleucine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166493	SO:0001438	SO:0001411	isoleucine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733626	SO:0001439	SO:0000104	proline	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166495	SO:0001439	SO:0001411	proline	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733628	SO:0001440	SO:0000104	tryptophan	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166497	SO:0001440	SO:0001411	tryptophan	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733630	SO:0001441	SO:0000104	phenylalanine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166499	SO:0001441	SO:0001411	phenylalanine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733632	SO:0001442	SO:0000104	methionine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166501	SO:0001442	SO:0001411	methionine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733634	SO:0001443	SO:0000104	glycine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166503	SO:0001443	SO:0001411	glycine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733636	SO:0001444	SO:0000104	serine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166505	SO:0001444	SO:0001411	serine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733638	SO:0001445	SO:0000104	threonine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166507	SO:0001445	SO:0001411	threonine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733640	SO:0001446	SO:0000104	tyrosine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166509	SO:0001446	SO:0001411	tyrosine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733642	SO:0001447	SO:0000104	cysteine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166511	SO:0001447	SO:0001411	cysteine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733644	SO:0001448	SO:0000104	glutamine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166513	SO:0001448	SO:0001411	glutamine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733646	SO:0001449	SO:0000104	asparagine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166515	SO:0001449	SO:0001411	asparagine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733648	SO:0001450	SO:0000104	lysine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166517	SO:0001450	SO:0001411	lysine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733650	SO:0001451	SO:0000104	arginine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166519	SO:0001451	SO:0001411	arginine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733652	SO:0001452	SO:0000104	histidine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166521	SO:0001452	SO:0001411	histidine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733654	SO:0001453	SO:0000104	aspartic_acid	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166523	SO:0001453	SO:0001411	aspartic_acid	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733656	SO:0001454	SO:0000104	glutamic_acid	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166525	SO:0001454	SO:0001411	glutamic_acid	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733658	SO:0001455	SO:0000104	selenocysteine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166527	SO:0001455	SO:0001411	selenocysteine	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	733660	SO:0001456	SO:0000104	pyrrolysine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166529	SO:0001456	SO:0001411	pyrrolysine	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]	SO	733662	SO:0001457	SO:0000001	transcribed_cluster	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]	SO	733663	SO:0001458	SO:0001410	unigene_cluster	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]	SO	733664	SO:0001459	SO:0000657	CRISPR	SO:0001411
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	733665	SO:0001460	SO:0000410	insulator_binding_site	SO:0000409
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	733666	SO:0001460	SO:0001055	insulator_binding_site	SO:0001679
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	733667	SO:0001461	SO:0000410	enhancer_binding_site	SO:0000409
3	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	733668	SO:0001461	SO:0000727	enhancer_binding_site	SO:0001055
3	"A comment about the sequence." [SO:ke]	\N	remark	SOFA	biosapiens	sequence	"A collection of contigs." [SO:ke]	SO	733669	SO:0001462	SO:0001082	contig_collection	SO:0000700
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	733670	SO:0001463	SO:0000655	lincRNA	SO:0000233
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	SO	733671	SO:0001464	SO:0000324	UST	SO:0000696
3	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	SOFA	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	733672	SO:0001465	SO:0000345	three_prime_UST	SO:0000324
3	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	SOFA	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	733673	SO:0001466	SO:0000345	five_prime_UST	SO:0000324
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	733674	SO:0001467	SO:0000324	RST	SO:0000696
3	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	733675	SO:0001468	SO:0000345	three_prime_RST	SO:0000324
3	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	\N	tag	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	733676	SO:0001469	SO:0000345	five_prime_RST	SO:0000324
3	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	\N	match	SOFA	SOFA	sequence	"A match against an UST sequence." [SO:nlw]	SO	733677	SO:0001470	SO:0000347	UST_match	SO:0000343
3	"A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]	\N	match	SOFA	SOFA	sequence	"A match against an RST sequence." [SO:nlw]	SO	733678	SO:0001471	SO:0000347	RST_match	SO:0000343
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A nucleotide match to a primer sequence." [SO:nlw]	SO	733679	SO:0001472	SO:0000343	primer_match	SO:0001410
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	733680	SO:0001473	SO:0000835	miRNA_antiguide	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	733681	SO:0001473	SO:0000835	miRNA_antiguide	SO:0000833
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	733682	SO:0001475	SO:0000185	outron	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	733683	SO:0001475	SO:0000833	outron	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	733684	SO:0001475	SO:0000833	outron	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	733685	SO:0001476	SO:0001235	natural_plasmid	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	733686	SO:0001476	SO:0001037	natural_plasmid	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	733687	SO:0001476	SO:0001037	natural_plasmid	SO:0001411
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	733688	SO:0001477	SO:0000155	gene_trap_construct	SO:0001235
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	733689	SO:0001477	SO:0000804	gene_trap_construct	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	733690	SO:0001477	SO:0000804	gene_trap_construct	SO:0001409
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	733691	SO:0001478	SO:0000155	promoter_trap_construct	SO:0001235
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	733692	SO:0001478	SO:0000804	promoter_trap_construct	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	733693	SO:0001478	SO:0000804	promoter_trap_construct	SO:0001409
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	733694	SO:0001479	SO:0000155	enhancer_trap_construct	SO:0001235
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	733695	SO:0001479	SO:0000804	enhancer_trap_construct	SO:0000001
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	733696	SO:0001479	SO:0000804	enhancer_trap_construct	SO:0001409
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	1166565	SO:0001480	SO:0000143	PAC_end	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	733698	SO:0001480	SO:0000149	PAC_end	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	733699	SO:0001480	SO:0000149	PAC_end	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	733700	SO:0001480	SO:0000149	PAC_end	SO:0000353
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	733701	SO:0001480	SO:0000440	PAC_end	SO:0000151
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	733702	SO:0001480	SO:0000440	PAC_end	SO:0001235
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]	SO	733703	SO:0001481	SO:0000695	RAPD	SO:0001409
3	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"" []	SO	733704	SO:0001482	SO:0000727	shadow_enhancer	SO:0001055
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SO	733705	SO:0001483	SO:0001059	SNV	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SO	733706	SO:0001483	SO:0001411	SNV	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	2441675	SO:0001484	SO:0001411	X_element_combinatorial_repeat	SO:0000001
3	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	733708	SO:0001484	SO:0000628	X_element_combinatorial_repeat	SO:0000830
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	2441676	SO:0001485	SO:0001411	Y_prime_element	SO:0000001
3	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	733710	SO:0001485	SO:0000628	Y_prime_element	SO:0000830
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]	SO	733711	SO:0001486	SO:0000905	standard_draft	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]	SO	733712	SO:0001487	SO:0000905	high_quality_draft	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]	SO	733713	SO:0001488	SO:0000905	improved_high_quality_draft	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]	SO	733714	SO:0001489	SO:0000905	annotation_directed_improved_draft	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]	SO	733715	SO:0001490	SO:0000905	noncontiguous_finished	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]	SO	733716	SO:0001491	SO:0000905	finished_genome	SO:0000733
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	733717	SO:0001492	SO:0005836	intronic_regulatory_region	SO:0000831
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	733718	SO:0001492	SO:0000835	intronic_regulatory_region	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	733719	SO:0001492	SO:0000835	intronic_regulatory_region	SO:0000833
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	733720	SO:0001493	SO:0001410	centromere_DNA_Element_I	SO:0000001
3	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	733721	SO:0001493	SO:0000577	centromere_DNA_Element_I	SO:0000628
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	733722	SO:0001494	SO:0001410	centromere_DNA_Element_II	SO:0000001
3	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	733723	SO:0001494	SO:0000577	centromere_DNA_Element_II	SO:0000628
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	733724	SO:0001495	SO:0001410	centromere_DNA_Element_III	SO:0000001
3	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	733725	SO:0001495	SO:0000577	centromere_DNA_Element_III	SO:0000628
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	2441683	SO:0001496	SO:0001411	telomeric_repeat	SO:0000001
3	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	733727	SO:0001496	SO:0000628	telomeric_repeat	SO:0000830
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	733728	SO:0001497	SO:0001410	X_element	SO:0000001
3	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	733729	SO:0001497	SO:0000628	X_element	SO:0000830
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	1166603	SO:0001498	SO:0000143	YAC_end	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	733731	SO:0001498	SO:0000149	YAC_end	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	733732	SO:0001498	SO:0000149	YAC_end	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	733733	SO:0001498	SO:0000149	YAC_end	SO:0000353
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	733734	SO:0001498	SO:0000440	YAC_end	SO:0000151
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	733735	SO:0001498	SO:0000440	YAC_end	SO:0001235
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The status of whole genome sequence." [DOI:10.1126]	SO	733736	SO:0001499	SO:0000733	whole_genome_sequence_status	SO:0000400
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]	SO	733737	SO:0001500	SO:0001411	heritable_phenotypic_marker	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An experimental feature with high sequence identity to another sequence." [SO:ke]	SO	733738	SO:0001502	SO:0000001	high_identity_region	SO:0000110
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]	SO	733739	SO:0001503	SO:0000831	processed_transcript	SO:0001411
3	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome variation derived from an event during meiosis." [SO:ke]	SO	733740	SO:0001504	SO:0001507	assortment_derived_variation	SO:0001260
3	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome variation derived from an event during meiosis." [SO:ke]	SO	733741	SO:0001504	SO:0001524	assortment_derived_variation	SO:0001506
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733742	SO:0001509	SO:0000733	chromosomal_variation_attribute	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	733743	SO:0001510	SO:0001508	intrachromosomal	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	733744	SO:0001511	SO:0001508	interchromosomal	SO:0000733
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A quality of a chromosomal insertion,." [SO:ke]	SO	733745	SO:0001512	SO:0000733	insertion_attribute	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	733746	SO:0001513	SO:0001508	tandem	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]	SO	733747	SO:0001514	SO:0001508	direct	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]	SO	733748	SO:0001515	SO:0001508	inverted	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The quality of a duplication where the new region exists independently of the original." [SO:ke]	SO	733749	SO:0001516	SO:0001508	free	SO:0000733
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733750	SO:0001517	SO:0000733	inversion_attribute	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	733751	SO:0001518	SO:0001508	pericentric	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	733752	SO:0001519	SO:0001508	paracentric	SO:0000733
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733753	SO:0001520	SO:0000733	translocaton_attribute	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	733754	SO:0001521	SO:0001508	reciprocal	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	733755	SO:0001522	SO:0001508	insertional	SO:0000733
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	733756	SO:0001523	SO:0000733	duplication_attribute	SO:0000400
3	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	733757	SO:0001524	SO:0001026	chromosomally_aberrant_genome	SO:0001260
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]	SO	733758	SO:0001525	SO:0000700	assembly_error_correction	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]	SO	733759	SO:0001526	SO:0000700	base_call_error_correction	SO:0001410
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	SO	733760	SO:0001527	SO:0000104	peptide_localization_signal	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	SO	1166624	SO:0001527	SO:0001411	peptide_localization_signal	SO:0000001
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	SO	733762	SO:0001528	SO:0000839	nuclear_localization_signal	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	SO	733763	SO:0001528	SO:0000839	nuclear_localization_signal	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	SO	733764	SO:0001529	SO:0000839	endosomal_localization_signal	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	SO	733765	SO:0001529	SO:0000839	endosomal_localization_signal	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	SO	733766	SO:0001530	SO:0000839	lysosomal_localization_signal	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	SO	733767	SO:0001530	SO:0000839	lysosomal_localization_signal	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	SO	733768	SO:0001531	SO:0000839	nuclear_export_signal	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	SO	733769	SO:0001531	SO:0000839	nuclear_export_signal	SO:0001411
3	"" []	\N	recombination_feature	\N	\N	sequence	"A region recognized by a recombinase." [SO:ke]	SO	733770	SO:0001532	SO:0000669	recombination_signal_sequence	SO:0000298
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	733771	SO:0001533	SO:0000835	cryptic_splice_site	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	733772	SO:0001533	SO:0000835	cryptic_splice_site	SO:0000833
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	SO	733773	SO:0001534	SO:0000839	nuclear_rim_localization_signal	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	SO	733774	SO:0001534	SO:0000839	nuclear_rim_localization_signal	SO:0001411
3	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	733775	SO:0001535	SO:0000101	p_element	SO:0001039
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which alters the level of a transcript." [SO:ke]	SO	733776	SO:0001540	SO:0001536	level_of_transcript_variant	SO:0001060
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	733777	SO:0001541	SO:0001538	decreased_transcript_level_variant	SO:0001536
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	733778	SO:0001542	SO:0001538	increased_transcript_level_variant	SO:0001536
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]	SO	733779	SO:0001543	SO:0001536	transcript_processing_variant	SO:0001060
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]	SO	733780	SO:0001544	SO:0001538	editing_variant	SO:0001536
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]	SO	733781	SO:0001545	SO:0001538	polyadenylation_variant	SO:0001536
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]	SO	733782	SO:0001546	SO:0001536	transcript_stability_variant	SO:0001060
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]	SO	733783	SO:0001547	SO:0001538	decreased_transcript_stability_variant	SO:0001536
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]	SO	733784	SO:0001548	SO:0001538	increased_transcript_stability_variant	SO:0001536
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]	SO	733785	SO:0001549	SO:0001536	transcription_variant	SO:0001060
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]	SO	733786	SO:0001550	SO:0001538	rate_of_transcription_variant	SO:0001536
3	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	733787	SO:0001551	SO:0001549	increased_transcription_rate_variant	SO:0001538
3	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	733788	SO:0001552	SO:0001549	decreased_transcription_rate_variant	SO:0001538
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]	SO	733789	SO:0001553	SO:0001536	translational_product_level_variant	SO:0001060
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	SO	733790	SO:0001554	SO:0001536	polypeptide_function_variant	SO:0001060
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]	SO	733791	SO:0001555	SO:0001539	decreased_translational_product_level	SO:0001536
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]	SO	733792	SO:0001556	SO:0001539	increased_translational_product_level	SO:0001536
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]	SO	733793	SO:0001557	SO:0001539	polypeptide_gain_of_function_variant	SO:0001536
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]	SO	733794	SO:0001558	SO:0001539	polypeptide_localization_variant	SO:0001536
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	SO	733795	SO:0001559	SO:0001539	polypeptide_loss_of_function_variant	SO:0001536
3	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]	SO	733796	SO:0001560	SO:0001554	inactive_ligand_binding_site	SO:0001539
3	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]	SO	733797	SO:0001561	SO:0001554	polypeptide_partial_loss_of_function	SO:0001539
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]	SO	733798	SO:0001562	SO:0001539	polypeptide_post_translational_processing_variant	SO:0001536
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where the structure of the gene is changed." [SO:ke]	SO	733799	SO:0001564	SO:0001537	gene_variant	SO:0001060
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby a two genes have become joined." [SO:ke]	SO	733800	SO:0001565	SO:0001878	gene_fusion	SO:0001537
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located within a regulatory region." [SO:ke]	SO	733801	SO:0001566	SO:0001537	regulatory_region_variant	SO:0001060
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	733802	SO:0001567	SO:0001580	stop_retained_variant	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	733803	SO:0001567	SO:0001580	stop_retained_variant	SO:0001968
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that changes the process of splicing." [SO:ke]	SO	733804	SO:0001568	SO:0001564	splicing_variant	SO:0001878
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	733805	SO:0001569	SO:0001576	cryptic_splice_site_variant	SO:0001564
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	SO	733806	SO:0001570	SO:0001568	cryptic_splice_acceptor	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	SO	733807	SO:0001571	SO:0001568	cryptic_splice_donor	SO:0001576
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby an exon is lost from the transcript." [SO:ke]	SO	733808	SO:0001572	SO:0001576	exon_loss_variant	SO:0001564
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	733809	SO:0001573	SO:0001576	intron_gain	SO:0001564
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	733810	SO:0001574	SO:0001568	splice_acceptor_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	733811	SO:0001574	SO:0001627	splice_acceptor_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	733812	SO:0001575	SO:0001568	splice_donor_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	733813	SO:0001575	SO:0001627	splice_donor_variant	SO:0001576
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that changes the structure of the transcript." [SO:ke]	SO	733814	SO:0001576	SO:0001878	transcript_variant	SO:0001537
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]	SO	733815	SO:0001577	SO:0001564	complex_transcript_variant	SO:0001878
5	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	1641251	SO:0001578	SO:0001580	stop_lost	SO:0001791
5	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	1641252	SO:0001578	SO:0001580	stop_lost	SO:0001968
9	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	2806650	SO:0001578	SO:0001878	stop_lost	SO:0001537
3	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	733819	SO:0001578	SO:0001650	stop_lost	SO:0001818
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	733820	SO:0001580	SO:0001576	coding_sequence_variant	SO:0001564
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	733821	SO:0001582	SO:0001791	initiator_codon_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	733822	SO:0001582	SO:0001968	initiator_codon_variant	SO:0001576
3	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	733823	SO:0001583	SO:0001650	missense_variant	SO:0001818
3	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	733824	SO:0001585	SO:0001992	conservative_missense_variant	SO:0001650
3	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	733825	SO:0001586	SO:0001992	non_conservative_missense_variant	SO:0001650
9	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	2885780	SO:0001587	SO:0001878	stop_gained	SO:0001537
3	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	733827	SO:0001587	SO:0001650	stop_gained	SO:0001818
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	733828	SO:0001589	SO:0001580	frameshift_variant	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	733829	SO:0001589	SO:0001580	frameshift_variant	SO:0001968
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	733830	SO:0001590	SO:0001791	terminator_codon_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	733831	SO:0001590	SO:0001968	terminator_codon_variant	SO:0001576
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	733832	SO:0001591	SO:0001818	frame_restoring_variant	SO:0001580
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	733833	SO:0001592	SO:0001818	minus_1_frameshift_variant	SO:0001580
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"" []	SO	733834	SO:0001593	SO:0001818	minus_2_frameshift_variant	SO:0001580
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	733835	SO:0001594	SO:0001818	plus_1_frameshift_variant	SO:0001580
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"" []	SO	733836	SO:0001595	SO:0001818	plus_2_frameshift_variant	SO:0001580
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]	SO	733837	SO:0001596	SO:0001564	transcript_secondary_structure_variant	SO:0001878
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]	SO	733838	SO:0001597	SO:0001576	compensatory_transcript_secondary_structure_variant	SO:0001564
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	SO	733839	SO:0001598	SO:0001878	translational_product_structure_variant	SO:0001537
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	733840	SO:0001599	SO:0001536	3D_polypeptide_structure_variant	SO:0001060
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	733841	SO:0001600	SO:0001539	complex_3D_structural_variant	SO:0001536
3	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]	SO	733842	SO:0001601	SO:0001539	conformational_change_variant	SO:0001536
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"" []	SO	733843	SO:0001602	SO:0001536	complex_change_of_translational_product_variant	SO:0001060
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	SO	733844	SO:0001603	SO:0001564	polypeptide_sequence_variant	SO:0001878
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]	SO	733845	SO:0001604	SO:0001598	amino_acid_deletion	SO:0001564
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]	SO	733846	SO:0001605	SO:0001598	amino_acid_insertion	SO:0001564
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	SO	733847	SO:0001606	SO:0001598	amino_acid_substitution	SO:0001564
3	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	SO	733848	SO:0001607	SO:0001603	conservative_amino_acid_substitution	SO:0001598
3	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	SO	733849	SO:0001608	SO:0001603	non_conservative_amino_acid_substitution	SO:0001598
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	SO	733850	SO:0001609	SO:0001598	elongated_polypeptide	SO:0001564
3	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	733851	SO:0001610	SO:0001603	elongated_polypeptide_C_terminal	SO:0001598
3	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	733852	SO:0001611	SO:0001603	elongated_polypeptide_N_terminal	SO:0001598
3	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	733853	SO:0001612	SO:0001609	elongated_in_frame_polypeptide_C_terminal	SO:0001603
3	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	733854	SO:0001613	SO:0001609	elongated_out_of_frame_polypeptide_C_terminal	SO:0001603
3	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	733855	SO:0001614	SO:0001609	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001603
3	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	\N	polypeptide_sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	733856	SO:0001615	SO:0001609	elongated_out_of_frame_polypeptide_N_terminal	SO:0001603
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]	SO	733857	SO:0001616	SO:0001598	polypeptide_fusion	SO:0001564
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]	SO	733858	SO:0001617	SO:0001598	polypeptide_truncation	SO:0001564
3	"A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]	\N	polypeptide_function_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]	SO	733859	SO:0001618	SO:0001559	inactive_catalytic_site	SO:0001554
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant of a non coding RNA gene." [SO:ke]	SO	733860	SO:0001619	SO:0001564	non_coding_transcript_variant	SO:0001878
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant located with the sequence of the mature miRNA." [SO:ke]	SO	733861	SO:0001620	SO:0001576	mature_miRNA_variant	SO:0001564
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A variant in a transcript that is the target of NMD." [SO:ke]	SO	733862	SO:0001621	SO:0001564	NMD_transcript_variant	SO:0001878
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	733863	SO:0001622	SO:0001576	UTR_variant	SO:0001564
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	733864	SO:0001623	SO:0001791	5_prime_UTR_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	733865	SO:0001623	SO:0001968	5_prime_UTR_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	733866	SO:0001624	SO:0001791	3_prime_UTR_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	733867	SO:0001624	SO:0001968	3_prime_UTR_variant	SO:0001576
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	1166724	SO:0001626	SO:0001580	incomplete_terminal_codon_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	1166725	SO:0001626	SO:0001580	incomplete_terminal_codon_variant	SO:0001968
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	733870	SO:0001626	SO:0001818	incomplete_terminal_codon_variant	SO:0001580
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant occurring within an intron." [SO:ke]	SO	733871	SO:0001627	SO:0001564	intron_variant	SO:0001878
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located in the intergenic region, between genes." [SO:ke]	SO	733872	SO:0001628	SO:0001537	intergenic_variant	SO:0001060
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	733873	SO:0001629	SO:0001576	splice_site_variant	SO:0001564
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]	SO	733874	SO:0001630	SO:0001576	splice_region_variant	SO:0001564
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located 5' of a gene." [SO:ke]	SO	733875	SO:0001631	SO:0001878	upstream_gene_variant	SO:0001537
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located 3' of a gene." [SO:ke]	SO	733876	SO:0001632	SO:0001878	downstream_gene_variant	SO:0001537
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located within 5 KB of the end of a gene." [SO:ke]	SO	733877	SO:0001633	SO:0001628	5KB_downstream_variant	SO:0001878
3	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A sequence variant located within a half KB of the end of a gene." [SO:ke]	SO	733878	SO:0001634	SO:0001632	500B_downstream_variant	SO:0001628
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located within 5KB 5' of a gene." [SO:ke]	SO	733879	SO:0001635	SO:0001628	5KB_upstream_variant	SO:0001878
3	"A sequence variant located in the intergenic region, between genes." [SO:ke]	\N	intergenic_variant	\N	\N	sequence	"A sequence variant located within 2KB 5' of a gene." [SO:ke]	SO	733880	SO:0001636	SO:0001631	2KB_upstream_variant	SO:0001628
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes for ribosomal RNA." [SO:ke]	SO	733881	SO:0001637	SO:0000704	rRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes for an piwi associated RNA." [SO:ke]	SO	733882	SO:0001638	SO:0000704	piRNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes an RNase P RNA." [SO:ke]	SO	733883	SO:0001639	SO:0000704	RNase_P_RNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes a RNase_MRP_RNA." [SO:ke]	SO	733884	SO:0001640	SO:0000704	RNase_MRP_RNA_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes large intervening non-coding RNA." [SO:ke]	SO	733885	SO:0001641	SO:0000704	lincRNA_gene	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill]	SO	733886	SO:0001642	SO:0000001	mathematically_defined_repeat	SO:0000110
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]	SO	733887	SO:0001643	SO:0000704	telomerase_RNA_gene	SO:0001411
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	733888	SO:0001644	SO:0000151	targeting_vector	SO:0000695
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	733889	SO:0001644	SO:0001235	targeting_vector	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	1679605	SO:0001644	SO:0000001	targeting_vector	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	1641311	SO:0001644	SO:0001409	targeting_vector	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A measurable sequence feature that varies within a population." [SO:db]	SO	733892	SO:0001645	SO:0000001	genetic_marker	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]	SO	733893	SO:0001646	SO:0001411	DArT_marker	SO:0000001
3	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SOFA	UTR	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	733894	SO:0001647	SO:0000204	kozak_sequence	SO:0000203
5	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	1641313	SO:0001647	SO:0000836	kozak_sequence	SO:0000234
5	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	1641314	SO:0001647	SO:0000836	kozak_sequence	SO:0000834
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transposon that is disrupted by the insertion of another element." [SO:ke]	SO	733897	SO:0001648	SO:0001039	nested_transposon	SO:0001037
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repeat that is disrupted by the insertion of another element." [SO:ke]	SO	733898	SO:0001649	SO:0001411	nested_repeat	SO:0000001
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	733899	SO:0001650	SO:0001580	inframe_variant	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	733900	SO:0001650	SO:0001580	inframe_variant	SO:0001968
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	733901	SO:0001653	SO:0000714	retinoic_acid_responsive_element	SO:0001683
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	733902	SO:0001653	SO:0001055	retinoic_acid_responsive_element	SO:0001679
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	733903	SO:0001654	SO:0000409	nucleotide_to_protein_binding_site	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	SO	733904	SO:0001655	SO:0001411	nucleotide_binding_site	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	SO	733905	SO:0001656	SO:0001411	metal_binding_site	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]	SO	733906	SO:0001657	SO:0001411	ligand_binding_site	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]	SO	733907	SO:0001658	SO:0000657	nested_tandem_repeat	SO:0001411
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"" []	SO	733908	SO:0001659	SO:0000714	promoter_element	SO:0001683
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"" []	SO	733909	SO:0001660	SO:0000713	core_promoter_element	SO:0000714
3	"" []	\N	promoter_element	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	733910	SO:0001661	SO:0001660	RNA_polymerase_II_TATA_box	SO:0001659
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	733911	SO:0001661	SO:0000170	RNA_polymerase_II_TATA_box	SO:0001203
3	"" []	\N	promoter_element	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	733912	SO:0001662	SO:0001660	RNA_polymerase_III_TATA_box	SO:0001659
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	733913	SO:0001662	SO:0001203	RNA_polymerase_III_TATA_box	SO:0000167
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	733914	SO:0001663	SO:0001659	BREd_motif	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	733915	SO:0001663	SO:0000170	BREd_motif	SO:0001203
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	733916	SO:0001664	SO:0001659	DCE	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	733917	SO:0001664	SO:0000170	DCE	SO:0001203
6	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	1644947	SO:0001665	SO:0000714	DCE_SI	SO:0001683
3	"" []	\N	promoter_element	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	733919	SO:0001665	SO:0001660	DCE_SI	SO:0001659
3	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	733920	SO:0001665	SO:0001669	DCE_SI	SO:0000170
6	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	1644948	SO:0001666	SO:0000714	DCE_SII	SO:0001683
3	"" []	\N	promoter_element	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	733922	SO:0001666	SO:0001660	DCE_SII	SO:0001659
3	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	733923	SO:0001666	SO:0001669	DCE_SII	SO:0000170
6	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	1644949	SO:0001667	SO:0000714	DCE_SIII	SO:0001683
3	"" []	\N	promoter_element	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	733925	SO:0001667	SO:0001660	DCE_SIII	SO:0001659
3	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	\N	RNApol_II_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	733926	SO:0001667	SO:0001669	DCE_SIII	SO:0000170
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	733927	SO:0001668	SO:0001659	proximal_promoter_element	SO:0000713
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	733928	SO:0001669	SO:0001203	RNApol_II_core_promoter	SO:0000167
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"" []	SO	733929	SO:0001670	SO:0001659	distal_promoter_element	SO:0000713
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	733930	SO:0001671	SO:0000752	bacterial_RNApol_promoter_sigma_70	SO:0001679
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"" []	SO	733931	SO:0001671	SO:0001203	bacterial_RNApol_promoter_sigma_70	SO:0000167
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	733932	SO:0001672	SO:0000752	bacterial_RNApol_promoter_sigma54	SO:0001679
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"" []	SO	733933	SO:0001672	SO:0001203	bacterial_RNApol_promoter_sigma54	SO:0000167
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	733934	SO:0001673	SO:0000714	minus_12_signal	SO:0001683
3	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	733935	SO:0001673	SO:0000613	minus_12_signal	SO:0000752
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	733936	SO:0001673	SO:0000613	minus_12_signal	SO:0001203
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	733937	SO:0001674	SO:0000714	minus_24_signal	SO:0001683
3	"" []	\N	gene_group_regulatory_region	SOFA	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	733938	SO:0001674	SO:0000613	minus_24_signal	SO:0000752
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	733939	SO:0001674	SO:0000613	minus_24_signal	SO:0001203
3	"" []	\N	promoter_element	\N	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	733940	SO:0001675	SO:0001660	A_box_type_1	SO:0001659
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	733941	SO:0001675	SO:0000171	A_box_type_1	SO:0001203
3	"" []	\N	promoter_element	\N	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	733942	SO:0001676	SO:0001660	A_box_type_2	SO:0001659
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	733943	SO:0001676	SO:0000171	A_box_type_2	SO:0001203
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	733944	SO:0001677	SO:0001659	intermediate_element	SO:0000713
3	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	733945	SO:0001677	SO:0000171	intermediate_element	SO:0001203
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	SO	733946	SO:0001678	SO:0000713	regulatory_promoter_element	SO:0000714
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SO	733947	SO:0001679	SO:0000831	transcription_regulatory_region	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of translation." [SO:ke]	SO	733948	SO:0001680	SO:0000831	translation_regulatory_region	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of recombination." [SO:ke]	SO	733949	SO:0001681	SO:0000831	recombination_regulatory_region	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]	SO	733950	SO:0001682	SO:0000831	replication_regulatory_region	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	SO	733951	SO:0001683	SO:0000001	sequence_motif	SO:0000110
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The score of an experimentally derived feature such as a p-value." [SO:ke]	SO	733952	SO:0001685	SO:0000733	score	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]	SO	733953	SO:0001686	SO:0000733	quality_value	SO:0000400
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	SO	733954	SO:0001687	SO:0001411	restriction_enzyme_recognition_site	SO:0000001
3	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	733955	SO:0001689	SO:0001688	five_prime_restriction_enzyme_junction	SO:0000699
3	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	733956	SO:0001689	SO:0001687	five_prime_restriction_enzyme_junction	SO:0001954
3	"A sequence_feature with an extent of zero." [SO:ke]	\N	junction	SOFA	\N	sequence	"" []	SO	733957	SO:0001690	SO:0001688	three_prime_restriction_enzyme_junction	SO:0000699
3	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"" []	SO	733958	SO:0001690	SO:0001687	three_prime_restriction_enzyme_junction	SO:0001954
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	733959	SO:0001691	SO:0001954	blunt_end_restriction_enzyme_cleavage_site	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	733960	SO:0001692	SO:0001954	sticky_end_restriction_enzyme_cleavage_site	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	733961	SO:0001693	SO:0000699	blunt_end_restriction_enzyme_cleavage_junction	SO:0000110
3	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	733962	SO:0001693	SO:0001687	blunt_end_restriction_enzyme_cleavage_junction	SO:0001954
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]	SO	733963	SO:0001694	SO:0000699	single_strand_restriction_enzyme_cleavage_site	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	SO	1173141	SO:0001695	SO:0001411	restriction_enzyme_single_strand_overhang	SO:0000001
3	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	SO	733965	SO:0001695	SO:0001687	restriction_enzyme_single_strand_overhang	SO:0001954
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]	SO	733966	SO:0001696	SO:0000001	experimentally_defined_binding_region	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]	SO	733967	SO:0001697	SO:0001410	ChIP_seq_region	SO:0000001
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	SO	733968	SO:0001698	SO:0000441	ASPE_primer	SO:0000696
3	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	SO	733969	SO:0001699	SO:0000441	dCAPS_primer	SO:0000696
3	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	733970	SO:0001700	SO:0100001	histone_modification	SO:0001067
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	2706899	SO:0001700	SO:0001411	histone_modification	SO:0000001
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	733972	SO:0001701	SO:0001089	histone_methylation_site	SO:0100001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	733973	SO:0001701	SO:0001720	histone_methylation_site	SO:0001411
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	733974	SO:0001702	SO:0001089	histone_acetylation_site	SO:0100001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	733975	SO:0001702	SO:0001720	histone_acetylation_site	SO:0001411
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	733976	SO:0001703	SO:0001702	H3K9_acetylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	733977	SO:0001704	SO:0001702	H3K14_acetylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733978	SO:0001705	SO:0001701	H3K4_monomethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733979	SO:0001706	SO:0001701	H3K4_trimethylation	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733980	SO:0001707	SO:0001701	H3K9_trimethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733981	SO:0001708	SO:0001701	H3K27_monomethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733982	SO:0001709	SO:0001701	H3K27_trimethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733983	SO:0001710	SO:0001701	H3K79_monomethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733984	SO:0001711	SO:0001701	H3K79_dimethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733985	SO:0001712	SO:0001701	H3K79_trimethylation_site	SO:0001700
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733986	SO:0001713	SO:0001700	H4K20_monomethylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733987	SO:0001713	SO:0001700	H4K20_monomethylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733988	SO:0001714	SO:0001700	H2BK5_monomethylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	733989	SO:0001714	SO:0001700	H2BK5_monomethylation_site	SO:0001720
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	SO	733990	SO:0001715	SO:0001679	ISRE	SO:0005836
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	733991	SO:0001716	SO:0001089	histone_ubiqitination_site	SO:0100001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	733992	SO:0001716	SO:0001720	histone_ubiqitination_site	SO:0001411
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	733993	SO:0001717	SO:0001700	H2B_ubiquitination_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	733994	SO:0001717	SO:0001700	H2B_ubiquitination_site	SO:0001720
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	733995	SO:0001718	SO:0001702	H3K18_acetylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	733996	SO:0001719	SO:0001702	H3K23_acylation_site	SO:0001700
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	SO	733997	SO:0001720	SO:0000001	epigenetically_modified_region	SO:0000110
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	733998	SO:0001721	SO:0001702	H3K27_acylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	733999	SO:0001722	SO:0001701	H3K36_monomethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	734000	SO:0001723	SO:0001701	H3K36_dimethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	734001	SO:0001724	SO:0001701	H3K36_trimethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	734002	SO:0001725	SO:0001701	H3K4_dimethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	734003	SO:0001726	SO:0001701	H3K27_dimethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	734004	SO:0001727	SO:0001701	H3K9_monomethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	734005	SO:0001728	SO:0001701	H3K9_dimethylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	734006	SO:0001729	SO:0001702	H4K16_acylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	734007	SO:0001730	SO:0001702	H4K5_acylation_site	SO:0001700
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	734008	SO:0001731	SO:0001702	H4K8_acylation_site	SO:0001700
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	734009	SO:0001732	SO:0001700	H3K27_methylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	734010	SO:0001732	SO:0001700	H3K27_methylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	734011	SO:0001733	SO:0001700	H3K36_methylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	734012	SO:0001733	SO:0001700	H3K36_methylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	734013	SO:0001734	SO:0001700	H3K4_methylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	734014	SO:0001734	SO:0001700	H3K4_methylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	734015	SO:0001735	SO:0001700	H3K79_methylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	734016	SO:0001735	SO:0001700	H3K79_methylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	734017	SO:0001736	SO:0001700	H3K9_methylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	734018	SO:0001736	SO:0001700	H3K9_methylation_site	SO:0001720
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	734019	SO:0001737	SO:0001089	histone_acylation_region	SO:0100001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	734020	SO:0001737	SO:0001720	histone_acylation_region	SO:0001411
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	734021	SO:0001738	SO:0001700	H4K_acylation_region	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	734022	SO:0001738	SO:0001700	H4K_acylation_region	SO:0001720
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene with a start codon other than AUG." [SO:xp]	SO	734023	SO:0001739	SO:0001411	gene_with_non_canonical_start_codon	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene with a translational start codon of CUG." [SO:mc]	SO	734024	SO:0001740	SO:0000704	gene_with_start_codon_CUG	SO:0001411
3	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	SOFA	sequence	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	SO	734025	SO:0001741	SO:0000842	pseudogenic_gene_segment	SO:0000704
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	SO	734026	SO:0001741	SO:0000842	pseudogenic_gene_segment	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR	sequence_feature	SOFA	SOFA	sequence	"A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]	SO	734027	SO:0001742	SO:0001059	copy_number_gain	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR	sequence_feature	SOFA	SOFA	sequence	"A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]	SO	734028	SO:0001743	SO:0001059	copy_number_loss	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm]	SO	734029	SO:0001745	SO:0001059	maternal_uniparental_disomy	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm]	SO	734030	SO:0001746	SO:0001059	paternal_uniparental_disomy	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb]	SO	734031	SO:0001747	SO:0000001	open_chromatin_region	SO:0000110
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734032	SO:0001748	SO:0000706	SL3_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734033	SO:0001749	SO:0000706	SL4_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734034	SO:0001750	SO:0000706	SL5_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734035	SO:0001751	SO:0000706	SL6_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734036	SO:0001752	SO:0000706	SL7_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734037	SO:0001753	SO:0000706	SL8_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734038	SO:0001754	SO:0000706	SL9_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734039	SO:0001755	SO:0000706	SL10_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734040	SO:0001756	SO:0000706	SL11_acceptor_site	SO:0001420
3	"Primary transcript region bordering trans-splice junction." [SO:ke]	\N	trans_splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	734041	SO:0001757	SO:0000706	SL12_acceptor_site	SO:0001420
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]	SO	734042	SO:0001758	SO:0000336	duplicated_pseudogene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]	SO	734043	SO:0001759	SO:0000336	unitary_pseudogene	SO:0001411
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	SO	734044	SO:0001760	SO:0001411	non_processed_pseudogene	SO:0000001
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]	SO	734045	SO:0001764	SO:0001761	unique_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734046	SO:0001765	SO:0001761	rare_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734047	SO:0001766	SO:0001761	polymorphic_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734048	SO:0001767	SO:0001761	common_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734049	SO:0001768	SO:0001761	fixed_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734050	SO:0001770	SO:0001761	benign_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734051	SO:0001771	SO:0001761	disease_associated_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734052	SO:0001772	SO:0001761	disease_causing_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734053	SO:0001773	SO:0001761	lethal_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734054	SO:0001774	SO:0001761	quantitative_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734055	SO:0001775	SO:0001761	maternal_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734056	SO:0001776	SO:0001761	paternal_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734057	SO:0001777	SO:0001761	somatic_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734058	SO:0001778	SO:0001761	germline_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734059	SO:0001779	SO:0001761	pedigree_specific_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734060	SO:0001780	SO:0001761	population_specific_variant	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734061	SO:0001781	SO:0001761	de_novo_variant	SO:0000400
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located within a transcription factor binding site." [EBI:fc]	SO	734062	SO:0001782	SO:0001878	TF_binding_site_variant	SO:0001537
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR	sequence_feature	SOFA	SOFA	sequence	"A structural sequence alteration or rearrangement encompassing one or more genome fragments." [NCBI:th, SO:ke]	SO	734063	SO:0001784	SO:0001059	complex_structural_alteration	SO:0000110
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	734064	SO:0001787	SO:0001568	splice_donor_5th_base_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	734065	SO:0001787	SO:0001627	splice_donor_5th_base_variant	SO:0001576
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	734066	SO:0001788	SO:0001410	U_box	SO:0000001
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	734067	SO:0001788	SO:0000180	U_box	SO:0000101
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	SO	734068	SO:0001789	SO:0001411	mating_type_region	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]	SO	734069	SO:0001790	SO:0001410	paired_end_fragment	SO:0000001
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that changes exon sequence." [SO:ke]	SO	734070	SO:0001791	SO:0001564	exon_variant	SO:0001878
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	734071	SO:0001792	SO:0001576	non_coding_transcript_exon_variant	SO:0001564
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	1166917	SO:0001793	SO:0000143	clone_end	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	734073	SO:0001793	SO:0000149	clone_end	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	734074	SO:0001793	SO:0000149	clone_end	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	734075	SO:0001793	SO:0000149	clone_end	SO:0000353
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	734076	SO:0001793	SO:0000695	clone_end	SO:0001409
3	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	734077	SO:0001794	SO:0000628	point_centromere	SO:0000830
3	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	734078	SO:0001795	SO:0000628	regional_centromere	SO:0000830
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	734079	SO:0001796	SO:0001410	regional_centromere_central_core	SO:0000001
3	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	734080	SO:0001796	SO:0000577	regional_centromere_central_core	SO:0000628
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repeat region found within the modular centromere." [SO:ke]	SO	734081	SO:0001797	SO:0001411	centromeric_repeat	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	734082	SO:0001798	SO:0000657	regional_centromere_inner_repeat_region	SO:0001411
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	734083	SO:0001798	SO:0000330	regional_centromere_inner_repeat_region	SO:0001410
3	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	734084	SO:0001798	SO:0001795	regional_centromere_inner_repeat_region	SO:0000577
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	734085	SO:0001799	SO:0000657	regional_centromere_outer_repeat_region	SO:0001411
3	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	734086	SO:0001799	SO:0000577	regional_centromere_outer_repeat_region	SO:0000628
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	SO	734087	SO:0001800	SO:0000233	tasiRNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a tasiRNA." [PMID:16145017]	SO	734088	SO:0001801	SO:0000185	tasiRNA_primary_transcript	SO:0000673
3	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]	SO	734089	SO:0001802	SO:0001543	increased_polyadenylation_variant	SO:0001538
3	"A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]	\N	transcript_function_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]	SO	734090	SO:0001803	SO:0001543	decreased_polyadenylation_variant	SO:0001538
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	734091	SO:0001804	SO:0000410	DDB_box	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	734092	SO:0001804	SO:0100002	DDB_box	SO:0100001
3	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	734093	SO:0001805	SO:0001067	destruction_box	SO:0100021
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	SO	734094	SO:0001806	SO:0000839	ER_retention_signal	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	SO	734095	SO:0001806	SO:0000839	ER_retention_signal	SO:0001411
3	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	734096	SO:0001807	SO:0001067	KEN_box	SO:0100021
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	SO	734097	SO:0001808	SO:0000839	mitochondrial_targeting_signal	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	SO	734098	SO:0001808	SO:0000839	mitochondrial_targeting_signal	SO:0001411
3	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	\N	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	734099	SO:0001809	SO:0001062	signal_anchor	SO:0100011
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	734100	SO:0001809	SO:0001527	signal_anchor	SO:0000839
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	734101	SO:0001810	SO:0000410	PIP_box	SO:0000409
3	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	734102	SO:0001810	SO:0100002	PIP_box	SO:0100001
3	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	734103	SO:0001811	SO:0100001	phosphorylation_site	SO:0001067
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	\N	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	734104	SO:0001812	SO:0001078	transmembrane_helix	SO:0001070
3	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	\N	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	734105	SO:0001812	SO:0001075	transmembrane_helix	SO:0001070
3	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	\N	membrane_structure	biosapiens	biosapiens	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	734106	SO:0001812	SO:0001075	transmembrane_helix	SO:0001071
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	SO	734107	SO:0001813	SO:0000839	vacuolar_sorting_signal	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	SO	734108	SO:0001813	SO:0000839	vacuolar_sorting_signal	SO:0001411
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734109	SO:0001815	SO:0001761	synonymous	SO:0000400
3	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	734110	SO:0001816	SO:0001761	non_synonymous	SO:0000400
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]	SO	734111	SO:0001817	SO:0000237	inframe	SO:0000733
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	734112	SO:0001818	SO:0001791	protein_altering_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	734113	SO:0001818	SO:0001968	protein_altering_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	734114	SO:0001819	SO:0001791	synonymous_variant	SO:0001576
3	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	734115	SO:0001819	SO:0001968	synonymous_variant	SO:0001576
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	734116	SO:0001820	SO:0001818	inframe_indel	SO:0001580
3	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	734117	SO:0001821	SO:0001650	inframe_insertion	SO:0001818
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	734118	SO:0001821	SO:0001907	inframe_insertion	SO:0001878
3	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	734119	SO:0001822	SO:0001650	inframe_deletion	SO:0001818
9	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	2885894	SO:0001822	SO:0001878	inframe_deletion	SO:0001537
3	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	734121	SO:0001823	SO:0001820	conservative_inframe_insertion	SO:0001650
3	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_elongation	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	734122	SO:0001823	SO:0001908	conservative_inframe_insertion	SO:0001907
3	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	734123	SO:0001824	SO:0001820	disruptive_inframe_insertion	SO:0001650
3	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	\N	feature_elongation	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	734124	SO:0001824	SO:0001908	disruptive_inframe_insertion	SO:0001907
3	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	734125	SO:0001825	SO:0001820	conservative_inframe_deletion	SO:0001650
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	734126	SO:0001825	SO:0001906	conservative_inframe_deletion	SO:0001878
3	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	734127	SO:0001826	SO:0001820	disruptive_inframe_deletion	SO:0001650
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	734128	SO:0001826	SO:0001906	disruptive_inframe_deletion	SO:0001878
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	1166975	SO:0001827	SO:0000143	mRNA_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	734130	SO:0001827	SO:0000149	mRNA_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	734131	SO:0001827	SO:0000149	mRNA_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	734132	SO:0001827	SO:0000149	mRNA_read	SO:0000353
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	1166980	SO:0001828	SO:0000143	genomic_DNA_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	734134	SO:0001828	SO:0000149	genomic_DNA_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	734135	SO:0001828	SO:0000149	genomic_DNA_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	734136	SO:0001828	SO:0000149	genomic_DNA_read	SO:0000353
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	734137	SO:0001829	SO:0000143	mRNA_contig	SO:0001410
3	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	734138	SO:0001829	SO:0000148	mRNA_contig	SO:0000719
3	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	734139	SO:0001829	SO:0000148	mRNA_contig	SO:0001876
6	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	1805756	SO:0001829	SO:0000353	mRNA_contig	SO:0001248
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]	SO	734141	SO:0001830	SO:0000695	AFLP_fragment	SO:0001409
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A match to a protein HMM such as pfam." [SO:ke]	SO	734142	SO:0001831	SO:0000343	protein_hmm_match	SO:0001410
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	SO	734143	SO:0001832	SO:0000104	immunoglobulin_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	SO	1166990	SO:0001832	SO:0001411	immunoglobulin_region	SO:0000001
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	734145	SO:0001833	SO:0000839	V_region	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	734146	SO:0001833	SO:0000839	V_region	SO:0001411
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	734147	SO:0001834	SO:0000839	C_region	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	734148	SO:0001834	SO:0000839	C_region	SO:0001411
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	734149	SO:0001835	SO:0000300	N_region	SO:0000299
3	"" []	\N	specific_recombination_site	\N	\N	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	734150	SO:0001836	SO:0000300	S_region	SO:0000299
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]	SO	734151	SO:0001837	SO:0001059	mobile_element_insertion	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]	SO	734152	SO:0001837	SO:0001411	mobile_element_insertion	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]	SO	734153	SO:0001838	SO:0001059	novel_sequence_insertion	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]	SO	734154	SO:0001838	SO:0001411	novel_sequence_insertion	SO:0000001
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	SO	734155	SO:0001839	SO:0000713	CSL_response_element	SO:0000714
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	734156	SO:0001840	SO:0001659	GATA_box	SO:0000713
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]	SO	734157	SO:0001841	SO:0001411	polymorphic_pseudogene	SO:0000001
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	SO	734158	SO:0001842	SO:0000713	AP_1_binding_site	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	SO	734159	SO:0001843	SO:0000713	CRE	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	SO	734160	SO:0001844	SO:0000713	CuRE	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	SO	734161	SO:0001845	SO:0000713	DRE	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	SO	734162	SO:0001846	SO:0000713	FLEX_element	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	SO	734163	SO:0001847	SO:0000713	forkhead_motif	SO:0000714
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	734164	SO:0001848	SO:0001659	homol_D_box	SO:0000713
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	SO	734165	SO:0001849	SO:0000713	homol_E_box	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	SO	734166	SO:0001850	SO:0000713	HSE	SO:0000714
3	"" []	\N	promoter_element	\N	\N	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	734167	SO:0001851	SO:0001660	iron_repressed_GATA_element	SO:0001659
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	SO	734168	SO:0001852	SO:0000713	mating_type_M_box	SO:0000714
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]	SO	734169	SO:0001853	SO:0000714	androgen_response_element	SO:0001683
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]	SO	734170	SO:0001854	SO:0000696	smFISH_probe	SO:0000695
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	SO	734171	SO:0001855	SO:0000713	MCB	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	SO	734172	SO:0001856	SO:0000713	CCAAT_motif	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	SO	734173	SO:0001857	SO:0000713	Ace2_UAS	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	SO	734174	SO:0001858	SO:0000713	TR_box	SO:0000714
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	SO	734175	SO:0001859	SO:0000713	STREP_motif	SO:0000714
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]	SO	734176	SO:0001860	SO:0000714	rDNA_intergenic_spacer_element	SO:0001683
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	SO	734177	SO:0001861	SO:0000713	sterol_regulatory_element	SO:0000714
3	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	satellite_DNA	SOFA	SOFA	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	734178	SO:0001862	SO:0000289	GT_dinucleotide_repeat	SO:0000005
3	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	satellite_DNA	SOFA	SOFA	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	734179	SO:0001863	SO:0000289	GTT_trinucleotide_repeat	SO:0000005
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]	SO	734180	SO:0001864	SO:0000714	Sap1_recognition_motif	SO:0001683
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	SO	734181	SO:0001865	SO:0000713	CDRE_motif	SO:0000714
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	734182	SO:0001866	SO:0000143	BAC_read_contig	SO:0001410
3	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	734183	SO:0001866	SO:0000148	BAC_read_contig	SO:0000719
3	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	734184	SO:0001866	SO:0000148	BAC_read_contig	SO:0001876
6	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	1805760	SO:0001866	SO:0000353	BAC_read_contig	SO:0001248
3	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	\N	clone	SOFA	\N	sequence	"A contig of BAC reads." [GMOD:ea]	SO	734186	SO:0001866	SO:0000440	BAC_read_contig	SO:0000151
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A contig of BAC reads." [GMOD:ea]	SO	734187	SO:0001866	SO:0000440	BAC_read_contig	SO:0001235
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene suspected of being involved in the expression of a trait." [GMOD:ea]	SO	734188	SO:0001867	SO:0001411	candidate_gene	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]	SO	734189	SO:0001868	SO:0000704	positional_candidate_gene	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]	SO	734190	SO:0001869	SO:0000704	functional_candidate_gene	SO:0001411
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	SO	734191	SO:0001870	SO:0000233	enhancerRNA	SO:0000673
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	SO	734192	SO:0001871	SO:0000713	PCB	SO:0000714
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	SO	734193	SO:0001872	SO:0000001	rearrangement_breakpoint	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]	SO	734194	SO:0001872	SO:0001059	rearrangement_breakpoint	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	SO	734195	SO:0001873	SO:0001411	interchromosomal_breakpoint	SO:0000001
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR	sequence	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	SO	734196	SO:0001873	SO:0001785	interchromosomal_breakpoint	SO:0001059
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	SO	734197	SO:0001874	SO:0001411	intrachromosomal_breakpoint	SO:0000001
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR	sequence	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	SO	734198	SO:0001874	SO:0001785	intrachromosomal_breakpoint	SO:0001059
3	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	734199	SO:0001875	SO:0000719	unassigned_supercontig	SO:0001876
4	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	1167042	SO:0001875	SO:0001876	unassigned_supercontig	SO:0000353
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SO	734201	SO:0001876	SO:0001248	partial_genomic_sequence_assembly	SO:0001410
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	SO	734202	SO:0001877	SO:0000233	lnc_RNA	SO:0000673
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature translocation where the region contains a transcript." [SO:ke]	SO	734203	SO:0001883	SO:0001537	transcript_translocation	SO:0001060
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature translocation where the region contains a regulatory region." [SO:ke]	SO	734204	SO:0001884	SO:0001537	regulatory_region_translocation	SO:0001060
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature translocation where the region contains a transcription factor binding site." [SO:ke]	SO	734205	SO:0001885	SO:0001881	TFBS_translocation	SO:0001537
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature fusion where the deletion brings together transcript regions." [SO:ke]	SO	734206	SO:0001886	SO:0001537	transcript_fusion	SO:0001060
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature fusion where the deletion brings together regulatory regions." [SO:ke]	SO	734207	SO:0001887	SO:0001537	regulatory_region_fusion	SO:0001060
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A fusion where the deletion brings together transcription factor binding sites." [SO:ke]	SO	734208	SO:0001888	SO:0001882	TFBS_fusion	SO:0001537
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature amplification of a region containing a transcript." [SO:ke]	SO	734209	SO:0001889	SO:0001537	transcript_amplification	SO:0001060
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]	SO	734210	SO:0001890	SO:0001537	transcript_regulatory_region_fusion	SO:0001060
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature amplification of a region containing a regulatory region." [SO:ke]	SO	734211	SO:0001891	SO:0001537	regulatory_region_amplification	SO:0001060
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature amplification of a region containing a transcription factor binding site." [SO:ke]	SO	734212	SO:0001892	SO:0001880	TFBS_amplification	SO:0001537
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]	SO	734213	SO:0001893	SO:0001537	transcript_ablation	SO:0001060
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]	SO	734214	SO:0001894	SO:0001537	regulatory_region_ablation	SO:0001060
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]	SO	734215	SO:0001895	SO:0001879	TFBS_ablation	SO:0001537
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	734216	SO:0001896	SO:0000836	transposable_element_CDS	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	734217	SO:0001896	SO:0000836	transposable_element_CDS	SO:0000834
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	734218	SO:0001896	SO:0001039	transposable_element_CDS	SO:0001037
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	1641592	SO:0001897	SO:0001411	transposable_element_pseudogene	SO:0000001
3	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	734220	SO:0001897	SO:0001039	transposable_element_pseudogene	SO:0001037
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	762598	SO:0001898	SO:0000657	dg_repeat	SO:0001411
3	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	734222	SO:0001898	SO:0001795	dg_repeat	SO:0000577
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	762599	SO:0001899	SO:0000657	dh_repeat	SO:0001411
3	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	\N	centromere	SOFA	\N	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	734225	SO:0001899	SO:0001795	dh_repeat	SO:0000577
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]	SO	734227	SO:0001900	SO:0000714	M26_binding_site	SO:0001683
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	734228	SO:0001901	SO:0001659	AACCCT_box	SO:0000713
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	734230	SO:0001902	SO:0000833	splice_region	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	734231	SO:0001902	SO:0000833	splice_region	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	762600	SO:0001902	SO:0000673	splice_region	SO:0000831
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	734233	SO:0001903	SO:0000655	intronic_lncRNA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	734234	SO:0001904	SO:0000655	antisense_lncRNA	SO:0000233
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]	SO	734235	SO:0001905	SO:0000673	regional_centromere_outer_repeat_transcript	SO:0000831
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]	SO	734236	SO:0001906	SO:0001537	feature_truncation	SO:0001060
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]	SO	734237	SO:0001907	SO:0001537	feature_elongation	SO:0001060
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	SO	734238	SO:0001908	SO:0001878	internal_feature_elongation	SO:0001537
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	734239	SO:0001909	SO:0001818	frameshift_elongation	SO:0001580
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	734240	SO:0001909	SO:0001907	frameshift_elongation	SO:0001878
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	734241	SO:0001910	SO:0001818	frameshift_truncation	SO:0001580
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	2707000	SO:0001910	SO:0001878	frameshift_truncation	SO:0001537
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]	SO	734243	SO:0001911	SO:0001537	copy_number_increase	SO:0001060
3	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]	SO	734244	SO:0001912	SO:0001537	copy_number_decrease	SO:0001060
3	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	734245	SO:0001913	SO:0000752	bacterial_RNApol_promoter_sigma_ecf	SO:0001679
3	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	734246	SO:0001913	SO:0001203	bacterial_RNApol_promoter_sigma_ecf	SO:0000167
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]	SO	734247	SO:0001914	SO:0000714	rDNA_replication_fork_barrier	SO:0001683
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]	SO	734248	SO:0001915	SO:0000001	transcription_start_cluster	SO:0000110
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]	SO	734249	SO:0001916	SO:0000696	CAGE_tag	SO:0000695
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]	SO	734250	SO:0001917	SO:0001410	CAGE_cluster	SO:0000001
3	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	734251	SO:0001918	SO:0000306	5_methylcytosine	SO:0000305
3	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	734252	SO:0001918	SO:0001963	5_methylcytosine	SO:0000305
3	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	734253	SO:0001919	SO:0000306	4_methylcytosine	SO:0000305
3	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	734254	SO:0001919	SO:0001963	4_methylcytosine	SO:0000305
3	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	734255	SO:0001920	SO:0000306	N6_methyladenine	SO:0000305
3	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	734256	SO:0001920	SO:0001962	N6_methyladenine	SO:0000305
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	734257	SO:0001921	SO:0000143	mitochondrial_contig	SO:0001410
3	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	734258	SO:0001921	SO:0000148	mitochondrial_contig	SO:0000719
3	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	734259	SO:0001921	SO:0000148	mitochondrial_contig	SO:0001876
6	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	1805767	SO:0001921	SO:0000353	mitochondrial_contig	SO:0001248
3	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	734261	SO:0001922	SO:0000719	mitochondrial_supercontig	SO:0001876
4	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	1167090	SO:0001922	SO:0001876	mitochondrial_supercontig	SO:0000353
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	734263	SO:0001923	SO:0000655	TERRA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	734264	SO:0001924	SO:0000655	ARRET	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	734265	SO:0001925	SO:0000655	ARIA	SO:0000233
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	734266	SO:0001926	SO:0000655	anti_ARRET	SO:0000233
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	SO	734267	SO:0001927	SO:0000233	telomeric_transcript	SO:0000673
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"A duplication of the distal region of a chromosome." [SO:bm]	SO	734268	SO:0001928	SO:0000667	distal_duplication	SO:0001059
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	DBVAR,SOFA	sequence	"A duplication of the distal region of a chromosome." [SO:bm]	SO	734269	SO:0001928	SO:0000667	distal_duplication	SO:0001411
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	1167100	SO:0001929	SO:0000143	mitochondrial_DNA_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	734271	SO:0001929	SO:0000149	mitochondrial_DNA_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	734272	SO:0001929	SO:0000149	mitochondrial_DNA_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	734273	SO:0001929	SO:0000149	mitochondrial_DNA_read	SO:0000353
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	1167105	SO:0001930	SO:0000143	chloroplast_DNA_read	SO:0001410
3	"A region of known length which may be used to manufacture a longer region." [SO:ke]	\N	assembly_component	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	734275	SO:0001930	SO:0000149	chloroplast_DNA_read	SO:0000143
3	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	\N	supercontig	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	734276	SO:0001930	SO:0000149	chloroplast_DNA_read	SO:0000148
3	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	734277	SO:0001930	SO:0000149	chloroplast_DNA_read	SO:0000353
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]	SO	1167109	SO:0001931	SO:0000001	consensus_gDNA	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]	SO	734279	SO:0001931	SO:0001410	consensus_gDNA	SO:0000001
3	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	734280	SO:0001932	SO:0001692	restriction_enzyme_five_prime_single_strand_overhang	SO:0001687
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	1641638	SO:0001932	SO:0001954	restriction_enzyme_five_prime_single_strand_overhang	SO:0001411
3	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	\N	restriction_enzyme_recognition_site	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	734282	SO:0001933	SO:0001692	restriction_enzyme_three_prime_single_strand_overhang	SO:0001687
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	1641640	SO:0001933	SO:0001954	restriction_enzyme_three_prime_single_strand_overhang	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]	SO	734284	SO:0001934	SO:0000657	monomeric_repeat	SO:0001411
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	734285	SO:0001935	SO:0001700	H3K20_trimethylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	734286	SO:0001935	SO:0001700	H3K20_trimethylation_site	SO:0001720
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	734287	SO:0001936	SO:0001702	H3K36_acetylation_site	SO:0001700
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	734288	SO:0001937	SO:0001700	H2BK12_acetylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	734289	SO:0001937	SO:0001700	H2BK12_acetylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	734290	SO:0001938	SO:0001700	H2AK5_acetylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	734291	SO:0001938	SO:0001700	H2AK5_acetylation_site	SO:0001720
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	734292	SO:0001939	SO:0001702	H4K12_acetylation_site	SO:0001700
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	734293	SO:0001940	SO:0001700	H2BK120_acetylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	734294	SO:0001940	SO:0001700	H2BK120_acetylation_site	SO:0001720
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	734295	SO:0001941	SO:0001702	H4K91_acetylation_site	SO:0001700
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	734296	SO:0001942	SO:0001700	H2BK20_acetylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	734297	SO:0001942	SO:0001700	H2BK20_acetylation_site	SO:0001720
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	734298	SO:0001943	SO:0001702	H3K4ac_acetylation_site	SO:0001700
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	734299	SO:0001944	SO:0001700	H2AK9_acetylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	734300	SO:0001944	SO:0001700	H2AK9_acetylation_site	SO:0001720
3	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	\N	histone_modification	\N	\N	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	734301	SO:0001945	SO:0001702	H3K56_acetylation_site	SO:0001700
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	734302	SO:0001946	SO:0001700	H2BK15_acetylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	734303	SO:0001946	SO:0001700	H2BK15_acetylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	734304	SO:0001947	SO:0001700	H3R2_monomethylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	734305	SO:0001947	SO:0001700	H3R2_monomethylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	734306	SO:0001948	SO:0001700	H3R2_dimethylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	734307	SO:0001948	SO:0001700	H3R2_dimethylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	734308	SO:0001949	SO:0001700	H4R3_dimethylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	734309	SO:0001949	SO:0001700	H4R3_dimethylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	734310	SO:0001950	SO:0001700	H4K4_trimethylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	734311	SO:0001950	SO:0001700	H4K4_trimethylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	734312	SO:0001951	SO:0001700	H3K23_dimethylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	734313	SO:0001951	SO:0001700	H3K23_dimethylation_site	SO:0001720
3	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	SO	734314	SO:0001952	SO:0001679	promoter_flanking_region	SO:0005836
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]	SO	734315	SO:0001953	SO:0001411	restriction_enzyme_assembly_scar	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region related to restriction enzyme function." [SO:ke]	SO	734316	SO:0001954	SO:0000001	restriction_enzyme_region	SO:0000110
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]	SO	734317	SO:0001955	SO:0000104	protein_stability_element	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]	SO	1167151	SO:0001955	SO:0001411	protein_stability_element	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide_region that  codes for a protease cleavage site." [SO:ke]	SO	734319	SO:0001956	SO:0000104	protease_site	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide_region that  codes for a protease cleavage site." [SO:ke]	SO	1167153	SO:0001956	SO:0001411	protease_site	SO:0000001
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	734321	SO:0001958	SO:0000835	lariat_intron	SO:0000185
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	734322	SO:0001958	SO:0000835	lariat_intron	SO:0000833
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	734323	SO:0001959	SO:0001659	TCT_motif	SO:0000713
3	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	734324	SO:0001960	SO:0000306	5_hydroxymethylcytosine	SO:0000305
3	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	modified_DNA_base	SOFA	\N	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	734325	SO:0001960	SO:0001963	5_hydroxymethylcytosine	SO:0000305
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	734326	SO:0001961	SO:0000305	5_formylcytosine	SO:0001236
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	734327	SO:0001961	SO:0000305	5_formylcytosine	SO:0001720
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified adenine DNA base feature." [SO:ke]	SO	734328	SO:0001962	SO:0001236	modified_adenine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified adenine DNA base feature." [SO:ke]	SO	734329	SO:0001962	SO:0001720	modified_adenine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified cytosine DNA base feature." [SO:ke]	SO	734330	SO:0001963	SO:0001236	modified_cytosine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified cytosine DNA base feature." [SO:ke]	SO	734331	SO:0001963	SO:0001720	modified_cytosine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified guanine DNA base feature." [SO:ke]	SO	734332	SO:0001964	SO:0001236	modified_guanine	SO:0001411
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified guanine DNA base feature." [SO:ke]	SO	734333	SO:0001964	SO:0001720	modified_guanine	SO:0001411
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	734334	SO:0001965	SO:0000305	8_oxoguanine	SO:0001236
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	734335	SO:0001965	SO:0000305	8_oxoguanine	SO:0001720
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	734336	SO:0001966	SO:0000305	5_carboxylcytosine	SO:0001236
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	734337	SO:0001966	SO:0000305	5_carboxylcytosine	SO:0001720
3	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	734338	SO:0001967	SO:0000305	8_oxoadenine	SO:0001236
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	734339	SO:0001967	SO:0000305	8_oxoadenine	SO:0001720
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant of a protein coding gene." [SO:ke]	SO	734340	SO:0001968	SO:0001564	coding_transcript_variant	SO:0001878
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	734341	SO:0001969	SO:0001576	coding_transcript_intron_variant	SO:0001564
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	734342	SO:0001970	SO:0001576	non_coding_transcript_intron_variant	SO:0001564
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	\N	sequence	"" []	SO	734343	SO:0001971	SO:0001655	zinc_finger_binding_site	SO:0000409
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	734344	SO:0001972	SO:0001700	histone_4_acylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	734345	SO:0001972	SO:0001700	histone_4_acylation_site	SO:0001720
3	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	734346	SO:0001973	SO:0001700	histone_3_acetylation_site	SO:0001089
3	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	734347	SO:0001973	SO:0001700	histone_3_acetylation_site	SO:0001720
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	SO	734348	SO:0001974	SO:0000713	CTCF_binding_site	SO:0000714
3	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]	SO	734349	SO:0001975	SO:0001687	five_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001954
3	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]	SO	734350	SO:0001976	SO:0001687	three_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001954
3	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	SO	734351	SO:0001977	SO:0000673	ribonuclease_site	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	SO	1641701	SO:0001977	SO:0001411	ribonuclease_site	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of  sequence where developer information is encoded." [SO:ke]	SO	1167185	SO:0001978	SO:0000001	signature	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of  sequence where developer information is encoded." [SO:ke]	SO	734354	SO:0001978	SO:0001409	signature	SO:0000001
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A motif that affects the stability of RNA." [PMID:22495308, SO:ke]	SO	734355	SO:0001979	SO:0000714	RNA_stability_element	SO:0001683
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	734356	SO:0001980	SO:0001659	G_box	SO:0000713
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	734357	SO:0001981	SO:0001659	L_box	SO:0000713
3	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	734358	SO:0001982	SO:0001659	I-box	SO:0000713
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	734359	SO:0001983	SO:0001622	5_prime_UTR_premature_start_codon_variant	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	734360	SO:0001983	SO:0001622	5_prime_UTR_premature_start_codon_variant	SO:0001968
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]	SO	734361	SO:0001984	SO:0005855	silent_mating_type_cassette_array	SO:0001411
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]	SO	734362	SO:0001985	SO:0000001	Okazaki_fragment	SO:0000110
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]	SO	734363	SO:0001986	SO:0001878	upstream_transcript_variant	SO:0001537
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"" []	SO	734364	SO:0001987	SO:0001878	downstream_transcript_variant	SO:0001537
3	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	734365	SO:0001988	SO:0001623	5_prime_UTR_premature_start_codon_gain_variant	SO:0001622
3	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	734366	SO:0001989	SO:0001623	5_prime_UTR_premature_start_codon_loss_variant	SO:0001622
3	"A transcript variant that is located within the UTR." [SO:ke]	\N	UTR_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	734367	SO:0001990	SO:0001623	five_prime_UTR_premature_start_codon_location_variant	SO:0001622
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]	SO	1167201	SO:0001991	SO:0000001	consensus_AFLP_fragment	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]	SO	734369	SO:0001991	SO:0001410	consensus_AFLP_fragment	SO:0000001
3	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	734370	SO:0001992	SO:0001818	nonsynonymous_variant	SO:0001580
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	734371	SO:0001993	SO:0000162	extended_cis_splice_site	SO:0000835
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	734372	SO:0001994	SO:0000188	intron_base_5	SO:0000835
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	1641721	SO:0001994	SO:0000835	intron_base_5	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	1641722	SO:0001994	SO:0000835	intron_base_5	SO:0000833
3	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	734375	SO:0001994	SO:0001419	intron_base_5	SO:0000162
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]	SO	734376	SO:0001995	SO:0001576	extended_intronic_splice_region_variant	SO:0001564
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	734377	SO:0001996	SO:0000188	extended_intronic_splice_region	SO:0000835
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	1167213	SO:0001996	SO:0000835	extended_intronic_splice_region	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	1167214	SO:0001996	SO:0000835	extended_intronic_splice_region	SO:0000833
3	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	734380	SO:0001997	SO:0000830	subtelomere	SO:0000340
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	734381	SO:0001997	SO:0000830	subtelomere	SO:0001411
3	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]	SO	734382	SO:0001998	SO:0000695	sgRNA	SO:0001409
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	734383	SO:0001999	SO:0000714	mating_type_region_motif	SO:0001683
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	734384	SO:0001999	SO:0005855	mating_type_region_motif	SO:0001411
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	734385	SO:0002000	SO:0000713	W_region	SO:0000714
3	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	734386	SO:0002000	SO:0001789	W_region	SO:0005855
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	734387	SO:0002001	SO:0000713	Y_region	SO:0000714
3	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	734388	SO:0002001	SO:0001789	Y_region	SO:0005855
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	734389	SO:0002002	SO:0000713	Z1_region	SO:0000714
3	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	734390	SO:0002002	SO:0001789	Z1_region	SO:0005855
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	734391	SO:0002003	SO:0000713	Z2_region	SO:0000714
3	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	734392	SO:0002003	SO:0001789	Z2_region	SO:0005855
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	734393	SO:0002004	SO:0000714	ARS_consensus_sequence	SO:0001683
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	734394	SO:0002004	SO:0000296	ARS_consensus_sequence	SO:0001235
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	734395	SO:0002004	SO:0000296	ARS_consensus_sequence	SO:0001411
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]	SO	734396	SO:0002005	SO:0000714	DSR_motif	SO:0001683
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	SO	734397	SO:0002006	SO:0000713	zinc_repressed_element	SO:0000714
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	SO	734398	SO:0002007	SO:0001059	MNV	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	SO	734399	SO:0002007	SO:0001411	MNV	SO:0000001
3	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	734400	SO:0002008	SO:0001583	rare_amino_acid_variant	SO:0001992
3	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	\N	missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	734401	SO:0002009	SO:0001586	selenocysteine_loss	SO:0001583
3	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	\N	missense_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	734402	SO:0002010	SO:0001586	pyrrolysine_loss	SO:0001583
3	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence." [SO:ke]	SO	734403	SO:0002011	SO:0001564	intragenic_variant	SO:0001878
5	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	1641748	SO:0002012	SO:0001580	start_lost	SO:0001791
5	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	1641749	SO:0002012	SO:0001580	start_lost	SO:0001968
3	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	734406	SO:0002012	SO:0001650	start_lost	SO:0001818
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	734407	SO:0002013	SO:0001622	5_prime_UTR_truncation	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	734408	SO:0002013	SO:0001622	5_prime_UTR_truncation	SO:0001968
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	734409	SO:0002014	SO:0001622	5_prime_UTR_elongation	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	734410	SO:0002014	SO:0001622	5_prime_UTR_elongation	SO:0001968
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	734411	SO:0002015	SO:0001622	3_prime_UTR_truncation	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	734412	SO:0002015	SO:0001622	3_prime_UTR_truncation	SO:0001968
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	734413	SO:0002016	SO:0001622	3_prime_UTR_elongation	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	734414	SO:0002016	SO:0001622	3_prime_UTR_elongation	SO:0001968
3	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located in a conserved intergenic region, between genes." [SO:ke]	SO	734415	SO:0002017	SO:0001878	conserved_intergenic_variant	SO:0001537
3	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A transcript variant occurring within a conserved region of an intron." [SO:ke]	SO	734416	SO:0002018	SO:0001576	conserved_intron_variant	SO:0001564
3	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	734417	SO:0002019	SO:0001580	start_retained_variant	SO:0001791
3	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	734418	SO:0002019	SO:0001580	start_retained_variant	SO:0001968
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]	SO	734419	SO:0002020	SO:0000714	boundary_element	SO:0001683
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]	SO	734420	SO:0002021	SO:0000714	mating_type_region_replication_fork_barrier	SO:0001683
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	SO	734421	SO:0002022	SO:0000233	priRNA	SO:0000673
3	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]	SO	734422	SO:0002023	SO:0000696	multiplexing_sequence_identifier	SO:0000695
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	734423	SO:0002024	SO:0000713	W_region	SO:0000714
3	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	734424	SO:0002024	SO:0001789	W_region	SO:0005855
3	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	SO	734425	SO:0002025	SO:0000714	cis_acting_homologous_chromosome_pairing_region	SO:0001683
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]	SO	734426	SO:0002026	SO:0000704	intein_encoding_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]	SO	1167263	SO:0002026	SO:0001411	intein_encoding_region	SO:0000001
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]	SO	734428	SO:0002027	SO:0000717	uORF	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]	SO	734429	SO:0002028	SO:0000717	sORF	SO:0001410
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]	SO	734430	SO:0002029	SO:0000717	tnaORF	SO:0001410
3	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	734431	SO:0002030	SO:0000713	X_region	SO:0000714
3	"A collection of related genes." [SO:ma]	\N	gene_group	SOFA	\N	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	734432	SO:0002030	SO:0001789	X_region	SO:0005855
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	SO	734433	SO:0002031	SO:0000233	shRNA	SO:0000673
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SO	734434	SO:0005836	SO:0001411	regulatory_region	SO:0000001
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	734435	SO:0005837	SO:0000483	U14_snoRNA_primary_transcript	SO:0000185
3	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	734436	SO:0005841	SO:0000275	methylation_guide_snoRNA	SO:0000655
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	SO	734437	SO:0005843	SO:0000233	rRNA_cleavage_RNA	SO:0000673
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	734438	SO:0005845	SO:0000833	exon_of_single_exon_gene	SO:0000673
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	734439	SO:0005845	SO:0000833	exon_of_single_exon_gene	SO:0001411
3	"" []	\N	gene_attribute	\N	\N	sequence	"" []	SO	734440	SO:0005847	SO:0000081	cassette_array_member	SO:0000401
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	734441	SO:0005848	SO:0000401	gene_cassette_member	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	734442	SO:0005849	SO:0000401	gene_subarray_member	SO:0000733
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	734443	SO:0005850	SO:0000409	primer_binding_site	SO:0001411
3	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	734444	SO:0005850	SO:0000180	primer_binding_site	SO:0000101
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]	SO	734445	SO:0005851	SO:0001411	gene_array	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]	SO	734446	SO:0005852	SO:0001411	gene_subarray	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]	SO	734447	SO:0005853	SO:0001411	gene_cassette	SO:0000001
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]	SO	734448	SO:0005854	SO:0001411	gene_cassette_array	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A collection of related genes." [SO:ma]	SO	734449	SO:0005855	SO:0000001	gene_group	SO:0000110
3	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	734450	SO:0005856	SO:0000483	selenocysteine_tRNA_primary_transcript	SO:0000185
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	734451	SO:0005857	SO:0000655	selenocysteinyl_tRNA	SO:0000233
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]	SO	734452	SO:0005858	SO:0001410	syntenic_region	SO:0000001
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	734453	SO:0100001	SO:0100021	biochemical_region_of_peptide	SO:0000839
3	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	734454	SO:0100002	SO:0001067	molecular_contact_region	SO:0100021
3	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	SO	734455	SO:0100003	SO:0000839	intrinsically_unstructured_polypeptide_region	SO:0000104
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	SO	734456	SO:0100003	SO:0000839	intrinsically_unstructured_polypeptide_region	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	734457	SO:0100004	SO:0001070	catmat_left_handed_three	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	734458	SO:0100005	SO:0001070	catmat_left_handed_four	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	734459	SO:0100006	SO:0001070	catmat_right_handed_three	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	734460	SO:0100007	SO:0001070	catmat_right_handed_four	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	734461	SO:0100008	SO:0001070	alpha_beta_motif	SO:0000839
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	1167306	SO:0100009	SO:0000839	lipoprotein_signal_peptide	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	1167307	SO:0100009	SO:0000839	lipoprotein_signal_peptide	SO:0001411
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	734464	SO:0100009	SO:0001063	lipoprotein_signal_peptide	SO:0000839
3	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	biosapiens	experimental_feature	SOFA	SOFA	sequence	"An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]	SO	734465	SO:0100010	SO:0000700	no_output	SO:0001410
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	SOFA	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	762601	SO:0100011	SO:0000104	cleaved_peptide_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens,SOFA	region	SOFA	SOFA	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	1260017	SO:0100011	SO:0001411	cleaved_peptide_region	SO:0000001
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	734470	SO:0100012	SO:0001070	peptide_coil	SO:0000839
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]	SO	734471	SO:0100013	SO:0000104	hydrophobic_region_of_peptide	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]	SO	1167312	SO:0100013	SO:0001411	hydrophobic_region_of_peptide	SO:0000001
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	1679624	SO:0100014	SO:0000839	n_terminal_region	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	1679625	SO:0100014	SO:0000839	n_terminal_region	SO:0001411
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	1173144	SO:0100014	SO:0001063	n_terminal_region	SO:0000839
3	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	734476	SO:0100014	SO:0001062	n_terminal_region	SO:0100011
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	734477	SO:0100014	SO:0001527	n_terminal_region	SO:0000839
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	1679628	SO:0100015	SO:0000839	c_terminal_region	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	1679629	SO:0100015	SO:0000839	c_terminal_region	SO:0001411
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	1173147	SO:0100015	SO:0001063	c_terminal_region	SO:0000839
3	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	734481	SO:0100015	SO:0001062	c_terminal_region	SO:0100011
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	734482	SO:0100015	SO:0001527	c_terminal_region	SO:0000839
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	1679632	SO:0100016	SO:0000839	central_hydrophobic_region_of_signal_peptide	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	1679633	SO:0100016	SO:0000839	central_hydrophobic_region_of_signal_peptide	SO:0001411
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	1173150	SO:0100016	SO:0001063	central_hydrophobic_region_of_signal_peptide	SO:0000839
3	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	biosapiens	cleaved_peptide_region	biosapiens,SOFA	biosapiens	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	734486	SO:0100016	SO:0001062	central_hydrophobic_region_of_signal_peptide	SO:0100011
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	734487	SO:0100016	SO:0001527	central_hydrophobic_region_of_signal_peptide	SO:0000839
3	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	734488	SO:0100017	SO:0100021	polypeptide_conserved_motif	SO:0000839
3	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	734489	SO:0100018	SO:0001067	polypeptide_binding_motif	SO:0100021
3	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	734490	SO:0100019	SO:0001067	polypeptide_catalytic_motif	SO:0100021
3	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	biosapiens	binding_site	biosapiens,SOFA	\N	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	734491	SO:0100020	SO:0001655	polypeptide_DNA_contact	SO:0000409
3	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	734492	SO:0100020	SO:0100001	polypeptide_DNA_contact	SO:0001067
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	734493	SO:0100021	SO:0000104	polypeptide_conserved_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	1167338	SO:0100021	SO:0001411	polypeptide_conserved_region	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	SO	734495	SO:1000002	SO:0000001	substitution	SO:0000110
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	734496	SO:1000005	SO:0001059	complex_substitution	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	734497	SO:1000005	SO:0001411	complex_substitution	SO:0000001
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	SOFA	sequence_alteration	SOFA	SOFA	sequence	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SO	734498	SO:1000008	SO:1000002	point_mutation	SO:0001059
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SO	734499	SO:1000008	SO:1000002	point_mutation	SO:0001411
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	734500	SO:1000009	SO:1000002	transition	SO:0001059
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	734501	SO:1000009	SO:1000002	transition	SO:0001411
3	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	734502	SO:1000010	SO:0001483	pyrimidine_transition	SO:1000002
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	734503	SO:1000011	SO:1000009	C_to_T_transition	SO:0001483
3	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	\N	transition	\N	\N	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	734504	SO:1000012	SO:1000010	C_to_T_transition_at_pCpG_site	SO:1000009
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"" []	SO	734505	SO:1000013	SO:1000009	T_to_C_transition	SO:0001483
3	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	734506	SO:1000014	SO:0001483	purine_transition	SO:1000002
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	734507	SO:1000015	SO:1000009	A_to_G_transition	SO:0001483
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	734508	SO:1000016	SO:1000009	G_to_A_transition	SO:0001483
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	734509	SO:1000017	SO:1000002	transversion	SO:0001059
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	734510	SO:1000017	SO:1000002	transversion	SO:0001411
3	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	734511	SO:1000018	SO:0001483	pyrimidine_to_purine_transversion	SO:1000002
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	734512	SO:1000019	SO:1000017	C_to_A_transversion	SO:0001483
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"" []	SO	734513	SO:1000020	SO:1000017	C_to_G_transversion	SO:0001483
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transversion from T to A." [SO:ke]	SO	734514	SO:1000021	SO:1000017	T_to_A_transversion	SO:0001483
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transversion from T to G." [SO:ke]	SO	734515	SO:1000022	SO:1000017	T_to_G_transversion	SO:0001483
3	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	734516	SO:1000023	SO:0001483	purine_to_pyrimidine_transversion	SO:1000002
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	734517	SO:1000024	SO:1000017	A_to_C_transversion	SO:0001483
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	734518	SO:1000025	SO:1000017	A_to_T_transversion	SO:0001483
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	734519	SO:1000026	SO:1000017	G_to_C_transversion	SO:0001483
3	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	734520	SO:1000027	SO:1000017	G_to_T_transversion	SO:0001483
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	734521	SO:1000028	SO:0000240	intrachromosomal_mutation	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	734522	SO:1000028	SO:0000240	intrachromosomal_mutation	SO:0001524
3	"" []	\N	chromosome_variation	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	734523	SO:1000029	SO:1000183	chromosomal_deletion	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	734524	SO:1000030	SO:1000183	chromosomal_inversion	SO:0000240
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	734525	SO:1000031	SO:0000240	interchromosomal_mutation	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	734526	SO:1000031	SO:0000240	interchromosomal_mutation	SO:0001524
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	SO	734527	SO:1000035	SO:0001059	duplication	SO:0000110
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	SO	734528	SO:1000035	SO:0001411	duplication	SO:0000001
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR,SOFA	sequence_feature	SOFA	SOFA	sequence	"A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	734529	SO:1000036	SO:0000001	inversion	SO:0000110
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	734530	SO:1000037	SO:0000240	chromosomal_duplication	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	734531	SO:1000037	SO:0000240	chromosomal_duplication	SO:0001524
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	734532	SO:1000038	SO:1000183	intrachromosomal_duplication	SO:0000240
3	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	\N	insertion	DBVAR,SOFA	\N	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	734533	SO:1000039	SO:1000035	direct_tandem_duplication	SO:0000667
3	"The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]	\N	insertion	DBVAR,SOFA	\N	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	734534	SO:1000040	SO:1000035	inverted_tandem_duplication	SO:0000667
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	762603	SO:1000041	SO:1000183	intrachromosomal_transposition	SO:0000240
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	734537	SO:1000041	SO:1000037	intrachromosomal_transposition	SO:1000183
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	734538	SO:1000042	SO:0000240	compound_chromosome	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	734539	SO:1000042	SO:0000240	compound_chromosome	SO:0001524
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	734540	SO:1000043	SO:1000031	Robertsonian_fusion	SO:1000183
3	"" []	\N	chromosome_variation	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	734541	SO:1000044	SO:1000183	chromosomal_translocation	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	734542	SO:1000045	SO:1000183	ring_chromosome	SO:0000240
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	734543	SO:1000046	SO:1000028	pericentric_inversion	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	734544	SO:1000047	SO:1000028	paracentric_inversion	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	734545	SO:1000048	SO:1000031	reciprocal_chromosomal_translocation	SO:1000183
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	734546	SO:1000136	SO:0000240	autosynaptic_chromosome	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	734547	SO:1000136	SO:0000240	autosynaptic_chromosome	SO:0001524
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	734548	SO:1000138	SO:1000183	homo_compound_chromosome	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	734549	SO:1000140	SO:1000183	hetero_compound_chromosome	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	734550	SO:1000141	SO:1000183	chromosome_fission	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	734551	SO:1000142	SO:1000183	dexstrosynaptic_chromosome	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	734552	SO:1000143	SO:1000183	laevosynaptic_chromosome	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	734553	SO:1000144	SO:1000183	free_duplication	SO:0000240
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	734554	SO:1000145	SO:1000028	free_ring_duplication	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	734555	SO:1000145	SO:1000037	free_ring_duplication	SO:1000183
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	734556	SO:1000146	SO:0000240	complex_chromosomal_mutation	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	734557	SO:1000146	SO:0000240	complex_chromosomal_mutation	SO:0001524
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	734558	SO:1000147	SO:1000028	deficient_translocation	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	734559	SO:1000147	SO:1000031	deficient_translocation	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	734561	SO:1000148	SO:1000031	inversion_cum_translocation	SO:1000183
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	762604	SO:1000148	SO:1000183	inversion_cum_translocation	SO:0000240
4	"" []	\N	chromosome_variation	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	1167419	SO:1000149	SO:1000183	bipartite_duplication	SO:0000240
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	734564	SO:1000149	SO:1000028	bipartite_duplication	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	734565	SO:1000149	SO:1000037	bipartite_duplication	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	734566	SO:1000150	SO:1000031	cyclic_translocation	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	734567	SO:1000151	SO:1000028	bipartite_inversion	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	734568	SO:1000152	SO:1000037	uninverted_insertional_duplication	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	734569	SO:1000153	SO:1000037	inverted_insertional_duplication	SO:1000183
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	734570	SO:1000154	SO:1000183	insertional_duplication	SO:0000240
3	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	734571	SO:1000155	SO:1000183	interchromosomal_transposition	SO:0000240
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	734572	SO:1000156	SO:0000453	inverted_interchromosomal_transposition	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	734573	SO:1000156	SO:1000031	inverted_interchromosomal_transposition	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	734574	SO:1000157	SO:0000453	uninverted_interchromosomal_transposition	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	734575	SO:1000157	SO:1000031	uninverted_interchromosomal_transposition	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	734576	SO:1000158	SO:0000453	inverted_intrachromosomal_transposition	SO:1000183
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1167431	SO:1000158	SO:1000028	inverted_intrachromosomal_transposition	SO:1000183
3	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	734578	SO:1000158	SO:1000038	inverted_intrachromosomal_transposition	SO:1000028
3	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	734579	SO:1000158	SO:1000038	inverted_intrachromosomal_transposition	SO:1000037
3	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	734580	SO:1000158	SO:1000030	inverted_intrachromosomal_transposition	SO:1000028
3	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	\N	interchromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	734581	SO:1000158	SO:1000044	inverted_intrachromosomal_transposition	SO:1000031
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	734582	SO:1000159	SO:0000453	uninverted_intrachromosomal_transposition	SO:1000183
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1167435	SO:1000159	SO:1000028	uninverted_intrachromosomal_transposition	SO:1000183
3	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	734584	SO:1000159	SO:1000038	uninverted_intrachromosomal_transposition	SO:1000028
3	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	734585	SO:1000159	SO:1000038	uninverted_intrachromosomal_transposition	SO:1000037
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	734586	SO:1000160	SO:1000037	unoriented_insertional_duplication	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	734587	SO:1000161	SO:0000453	unoriented_interchromosomal_transposition	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	734588	SO:1000161	SO:1000031	unoriented_interchromosomal_transposition	SO:1000183
3	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	734589	SO:1000162	SO:0000453	unoriented_intrachromosomal_transposition	SO:1000183
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1167440	SO:1000162	SO:1000028	unoriented_intrachromosomal_transposition	SO:1000183
3	"A chromosomal structure variation within a single chromosome." [SO:ke]	\N	intrachromosomal_mutation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	734591	SO:1000162	SO:1000038	unoriented_intrachromosomal_transposition	SO:1000028
3	"An extra chromosome." [SO:ke]	\N	chromosomal_duplication	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	734592	SO:1000162	SO:1000038	unoriented_intrachromosomal_transposition	SO:1000037
3	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"" []	SO	734593	SO:1000170	SO:0000240	uncharacterised_chromosomal_mutation	SO:0001507
3	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"" []	SO	734594	SO:1000170	SO:0000240	uncharacterised_chromosomal_mutation	SO:0001524
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	762605	SO:1000171	SO:1000183	deficient_inversion	SO:0000240
3	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	DBVAR	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	SO	734597	SO:1000173	SO:0000667	tandem_duplication	SO:0001059
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	DBVAR	biological_region	SOFA	DBVAR,SOFA	sequence	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	SO	734598	SO:1000173	SO:0000667	tandem_duplication	SO:0001411
3	"" []	\N	chromosome_variation	\N	\N	sequence	"" []	SO	734599	SO:1000175	SO:1000183	partially_characterised_chromosomal_mutation	SO:0000240
3	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	734600	SO:1000182	SO:0001507	chromosome_number_variation	SO:0001260
3	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	734601	SO:1000182	SO:0001524	chromosome_number_variation	SO:0001506
3	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	734602	SO:1000183	SO:0001507	chromosome_structure_variation	SO:0001260
3	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"" []	SO	734603	SO:1000183	SO:0001524	chromosome_structure_variation	SO:0001506
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is alternatively spliced." [SO:xp]	SO	734604	SO:1001187	SO:0000831	alternatively_spliced_transcript	SO:0001411
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]	SO	734605	SO:1001188	SO:0000401	encodes_1_polypeptide	SO:0000733
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	SO	734606	SO:1001189	SO:0000401	encodes_greater_than_1_polypeptide	SO:0000733
3	"A gene that encodes more than one transcript." [SO:ke]	\N	encodes_alternately_spliced_transcripts	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]	SO	734607	SO:1001190	SO:1001189	encodes_different_polypeptides_different_stop	SO:0000463
3	"A gene that encodes more than one transcript." [SO:ke]	\N	encodes_alternately_spliced_transcripts	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]	SO	734608	SO:1001191	SO:1001189	encodes_overlapping_peptides_different_start	SO:0000463
3	"" []	\N	gene_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]	SO	734609	SO:1001192	SO:0000463	encodes_disjoint_polypeptides	SO:0000401
3	"A gene that encodes more than one transcript." [SO:ke]	\N	encodes_alternately_spliced_transcripts	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]	SO	734610	SO:1001193	SO:1001189	encodes_overlapping_polypeptides_different_start_and_stop	SO:0000463
3	"" []	\N	gene_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	SO	734611	SO:1001195	SO:0000463	encodes_overlapping_peptides	SO:0000401
3	"A gene located in mitochondrial sequence." [SO:xp]	\N	mt_gene	\N	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	734612	SO:1001196	SO:0000089	cryptogene	SO:0000088
3	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	734613	SO:1001196	SO:0000742	cryptogene	SO:0001235
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	1641936	SO:1001196	SO:0000704	cryptogene	SO:0001411
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	\N	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	734615	SO:1001197	SO:0000078	dicistronic_primary_transcript	SO:0000673
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	762606	SO:1001197	SO:0000673	dicistronic_primary_transcript	SO:0000831
3	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	734618	SO:1001217	SO:0000401	member_of_regulon	SO:0000733
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	734619	SO:1001246	SO:0000836	CDS_independently_known	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	734620	SO:1001246	SO:0000836	CDS_independently_known	SO:0000834
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	734621	SO:1001247	SO:0000316	orphan_CDS	SO:0000836
4	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	1167471	SO:1001249	SO:0000316	CDS_supported_by_domain_match_data	SO:0000836
3	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	734623	SO:1001249	SO:1001254	CDS_supported_by_domain_match_data	SO:0000316
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	762607	SO:1001251	SO:0000836	CDS_supported_by_sequence_similarity_data	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	762608	SO:1001251	SO:0000836	CDS_supported_by_sequence_similarity_data	SO:0000834
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	734627	SO:1001254	SO:0000836	CDS_predicted	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	734628	SO:1001254	SO:0000836	CDS_predicted	SO:0000834
4	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	1167478	SO:1001259	SO:0000316	CDS_supported_by_EST_or_cDNA_data	SO:0000836
3	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	\N	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	734630	SO:1001259	SO:1001254	CDS_supported_by_EST_or_cDNA_data	SO:0000316
3	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	\N	five_prime_UTR	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	734631	SO:1001260	SO:0000139	internal_Shine_Dalgarno_sequence	SO:0000204
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	734632	SO:1001260	SO:0000139	internal_Shine_Dalgarno_sequence	SO:0000836
6	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2082573	SO:1001260	SO:0000836	internal_Shine_Dalgarno_sequence	SO:0000234
6	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2082574	SO:1001260	SO:0000836	internal_Shine_Dalgarno_sequence	SO:0000834
3	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	734635	SO:1001261	SO:0000233	recoded_mRNA	SO:0000673
3	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"An attribute describing a translational frameshift of -1." [SO:ke]	SO	734636	SO:1001262	SO:0000881	minus_1_translationally_frameshifted	SO:0000863
3	"An attribute describing an mRNA feature." [SO:ke]	\N	mRNA_attribute	\N	\N	sequence	"An attribute describing a translational frameshift of +1." [SO:ke]	SO	734637	SO:1001263	SO:0000881	plus_1_translationally_frameshifted	SO:0000863
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	762609	SO:1001264	SO:0000233	mRNA_recoded_by_translational_bypass	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	762610	SO:1001265	SO:0000233	mRNA_recoded_by_codon_redefinition	SO:0000673
3	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	734642	SO:1001268	SO:0000234	recoding_stimulatory_region	SO:0000233
3	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	734643	SO:1001268	SO:0000834	recoding_stimulatory_region	SO:0000833
3	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	\N	codon	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	734644	SO:1001269	SO:0000318	four_bp_start_codon	SO:0000360
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	734645	SO:1001271	SO:0000188	archaeal_intron	SO:0000835
3	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	734646	SO:1001272	SO:0000188	tRNA_intron	SO:0000835
3	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	\N	codon	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	734647	SO:1001273	SO:0000318	CTG_start_codon	SO:0000360
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	734648	SO:1001274	SO:0000836	SECIS_element	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	734649	SO:1001274	SO:0000836	SECIS_element	SO:0000834
3	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]	SO	734650	SO:1001275	SO:0000001	retron	SO:0000110
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	734651	SO:1001277	SO:0000836	three_prime_recoding_site	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	734652	SO:1001277	SO:0000836	three_prime_recoding_site	SO:0000834
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	734653	SO:1001279	SO:1001268	three_prime_stem_loop_structure	SO:0000836
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	734654	SO:1001280	SO:0000836	five_prime_recoding_site	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	734655	SO:1001280	SO:0000836	five_prime_recoding_site	SO:0000834
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	734656	SO:1001281	SO:1001268	flanking_three_prime_quadruplet_recoding_signal	SO:0000836
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	734657	SO:1001282	SO:1001268	UAG_stop_codon_signal	SO:0000836
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	734658	SO:1001283	SO:1001268	UAA_stop_codon_signal	SO:0000836
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]	SO	734659	SO:1001284	SO:0001411	regulon	SO:0000001
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	734660	SO:1001285	SO:1001268	UGA_stop_codon_signal	SO:0000836
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	734661	SO:1001286	SO:1001268	three_prime_repeat_recoding_signal	SO:0000836
3	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	\N	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	734662	SO:1001287	SO:1001268	distant_three_prime_recoding_signal	SO:0000836
3	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	734663	SO:1001288	SO:0000836	stop_codon_signal	SO:0000234
3	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	734664	SO:1001288	SO:0000836	stop_codon_signal	SO:0000834
3	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]	SO	734665	SO:2000061	SO:0001409	databank_entry	SO:0000001
3	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	SO	734666	SO:3000000	SO:0000704	gene_segment	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	SO	1167522	SO:3000000	SO:0001411	gene_segment	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]	SO	1164776	SO:0000003	SO:0000001	G_quartet	SO:0000110
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"" []	SO	1164777	SO:0000004	SO:0000833	interior_coding_exon	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"" []	SO	1164778	SO:0000004	SO:0000833	interior_coding_exon	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164779	SO:0000005	SO:0001411	satellite_DNA	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region amplified by a PCR reaction." [SO:ke]	SO	1164780	SO:0000006	SO:0000001	PCR_product	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	2731399	SO:0000007	SO:0001410	read_pair	SO:0000001
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	1259830	SO:0000007	SO:0000719	read_pair	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	\N	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	1805580	SO:0000007	SO:0001876	read_pair	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	2452722	SO:0000007	SO:0001248	read_pair	SO:0001410
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	SO	1164785	SO:0000012	SO:0000673	scRNA_primary_transcript	SO:0000831
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SO	1164786	SO:0000013	SO:0000673	scRNA	SO:0000831
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	1164787	SO:0000014	SO:0000713	INR_motif	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	1164788	SO:0000014	SO:0001203	INR_motif	SO:0000167
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	1164789	SO:0000015	SO:0000713	DPE_motif	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	1164790	SO:0000015	SO:0001203	DPE_motif	SO:0000167
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	1164791	SO:0000016	SO:0000713	BREu_motif	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	1164792	SO:0000016	SO:0001203	BREu_motif	SO:0000167
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	1164793	SO:0000017	SO:0001683	PSE_motif	SO:0001411
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	1164794	SO:0000017	SO:0001679	PSE_motif	SO:0005836
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	SO	1164795	SO:0000020	SO:0001683	RNA_internal_loop	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	SO	1164796	SO:0000021	SO:0000714	asymmetric_RNA_internal_loop	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]	SO	1164797	SO:0000022	SO:0001683	A_minor_RNA_motif	SO:0001411
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	1164798	SO:0000023	SO:0000715	K_turn_RNA_motif	SO:0000714
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	SOFA	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	1164799	SO:0000024	SO:0000715	sarcin_like_RNA_motif	SO:0000714
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	SO	1164800	SO:0000025	SO:0000714	symmetric_RNA_internal_loop	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1164801	SO:0000026	SO:0001683	RNA_junction_loop	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"" []	SO	1164802	SO:0000027	SO:0000714	RNA_hook_turn	SO:0001683
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1164803	SO:0000028	SO:0000001	base_pair	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]	SO	1164804	SO:0000029	SO:0001411	WC_base_pair	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A type of non-canonical base-pairing." [PMID:12177293]	SO	1164805	SO:0000030	SO:0001411	sugar_edge_base_pair	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	1164806	SO:0000031	SO:0001409	aptamer	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]	SO	1164807	SO:0000032	SO:0000695	DNA_aptamer	SO:0001409
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	1164808	SO:0000033	SO:0000695	RNA_aptamer	SO:0001409
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]	SO	1164809	SO:0000034	SO:0000695	morpholino_oligo	SO:0001409
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	1164810	SO:0000035	SO:0000833	riboswitch	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	1164811	SO:0000035	SO:0000833	riboswitch	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	1259833	SO:0000035	SO:0000673	riboswitch	SO:0000831
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	1164813	SO:0000036	SO:0000340	matrix_attachment_site	SO:0001235
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	2080935	SO:0000036	SO:0001411	matrix_attachment_site	SO:0000001
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	1164815	SO:0000037	SO:0001679	locus_control_region	SO:0005836
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A clone of a DNA region of a genome." [SO:ma]	SO	1164816	SO:0000040	SO:0001409	genomic_clone	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]	SO	1164817	SO:0000043	SO:0000001	processed_pseudogene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A pseudogene caused by unequal crossing over at recombination." [SO:ke]	SO	1164818	SO:0000044	SO:0001411	pseudogene_by_unequal_crossing_over	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	SO	1164819	SO:0000051	SO:0001409	probe	SO:0000001
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	1164820	SO:0000054	SO:0001507	aneuploid	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	1164821	SO:0000054	SO:0001524	aneuploid	SO:0001506
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	1164822	SO:0000055	SO:0000240	hyperploid	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	1164823	SO:0000055	SO:0000240	hyperploid	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	1164824	SO:0000056	SO:0000240	hypoploid	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	1164825	SO:0000056	SO:0000240	hypoploid	SO:0001524
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SO	1164826	SO:0000057	SO:0005836	operator	SO:0000831
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SO	1164827	SO:0000059	SO:0000409	nuclease_binding_site	SO:0001411
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"" []	SO	1164828	SO:0000060	SO:0000240	compound_chromosome_arm	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"" []	SO	1164829	SO:0000060	SO:0000240	compound_chromosome_arm	SO:0001524
4	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	SO	1164830	SO:0000061	SO:0000410	restriction_enzyme_binding_site	SO:0000409
5	"" []	\N	chromosome_variation	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	1259834	SO:0000062	SO:1000183	deficient_intrachromosomal_transposition	SO:0000240
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	1164833	SO:0000062	SO:1000037	deficient_intrachromosomal_transposition	SO:1000183
4	"" []	\N	chromosome_variation	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	1164834	SO:0000063	SO:1000183	deficient_interchromosomal_transposition	SO:0000240
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	1164835	SO:0000065	SO:0001507	free_chromosome_arm	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	1164836	SO:0000065	SO:0001524	free_chromosome_arm	SO:0001506
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]	SO	1164837	SO:0000068	SO:0000733	overlapping	SO:0000400
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	SO	1164838	SO:0000069	SO:0000401	inside_intron	SO:0000733
4	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]	SO	1164839	SO:0000070	SO:0000067	inside_intron_antiparallel	SO:0000401
4	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]	SO	1164840	SO:0000071	SO:0000067	inside_intron_parallel	SO:0000401
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]	SO	1164841	SO:0000073	SO:0000401	five_prime_three_prime_overlap	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]	SO	1164842	SO:0000074	SO:0000401	five_prime_five_prime_overlap	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]	SO	1164843	SO:0000075	SO:0000401	three_prime_three_prime_overlap	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]	SO	1164844	SO:0000076	SO:0000401	three_prime_five_prime_overlap	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]	SO	1164845	SO:0000077	SO:0000401	antisense	SO:0000733
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is polycistronic." [SO:xp]	SO	1164846	SO:0000078	SO:0001411	polycistronic_transcript	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is dicistronic." [SO:ke]	SO	1259835	SO:0000079	SO:0001411	dicistronic_transcript	SO:0000001
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1164848	SO:0000080	SO:0000733	operon_member	SO:0000400
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from nuclear sequence." [SO:xp]	SO	1164849	SO:0000087	SO:0000001	nuclear_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene located in mitochondrial sequence." [SO:xp]	SO	1164850	SO:0000088	SO:0000001	mt_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene located in kinetoplast sequence." [SO:xp]	SO	1164851	SO:0000089	SO:0001411	kinetoplast_gene	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from plastid sequence." [SO:xp]	SO	1164852	SO:0000090	SO:0000001	plastid_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from apicoplast sequence." [SO:xp]	SO	1164853	SO:0000091	SO:0001411	apicoplast_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from chloroplast sequence." [SO:xp]	SO	1164854	SO:0000092	SO:0001411	ct_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from chromoplast_sequence." [SO:xp]	SO	1164855	SO:0000093	SO:0001411	chromoplast_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from cyanelle sequence." [SO:xp]	SO	1164856	SO:0000094	SO:0001411	cyanelle_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plastid gene from leucoplast sequence." [SO:xp]	SO	1164857	SO:0000095	SO:0001411	leucoplast_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene from proplastid sequence." [SO:ke]	SO	1164858	SO:0000096	SO:0001411	proplastid_gene	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from nucleomorph sequence." [SO:xp]	SO	1164859	SO:0000097	SO:0000001	nucleomorph_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from plasmid sequence." [SO:xp]	SO	1164860	SO:0000098	SO:0000001	plasmid_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from proviral sequence." [SO:xp]	SO	1164861	SO:0000099	SO:0000001	proviral_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A proviral gene with origin endogenous retrovirus." [SO:xp]	SO	1164862	SO:0000100	SO:0001411	endogenous_retroviral_gene	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	SO	1639787	SO:0000101	SO:0000001	transposable_element	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	SO	1164864	SO:0000101	SO:0001411	transposable_element	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A match to an EST or cDNA sequence." [SO:ke]	SO	1164865	SO:0000102	SO:0001410	expressed_sequence_match	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	1259836	SO:0000103	SO:0001409	clone_insert_end	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	SO	1164868	SO:0000105	SO:0001235	chromosome_arm	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]	SO	1679545	SO:0000105	SO:0000001	chromosome_arm	SO:0000110
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"" []	SO	1164870	SO:0000107	SO:0000696	sequencing_primer	SO:0000695
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA with a frameshift." [SO:xp]	SO	1164871	SO:0000108	SO:0000673	mRNA_with_frameshift	SO:0000831
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	1679546	SO:0000111	SO:0000001	transposable_element_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	1164873	SO:0000111	SO:0001037	transposable_element_gene	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]	SO	1164874	SO:0000111	SO:0001037	transposable_element_gene	SO:0001411
4	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	SO	1164875	SO:0000112	SO:0000695	primer	SO:0001409
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A viral sequence which has integrated into a host genome." [SO:ke]	SO	1639796	SO:0000113	SO:0000001	proviral_region	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A viral sequence which has integrated into a host genome." [SO:ke]	SO	1164877	SO:0000113	SO:0001411	proviral_region	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	1164878	SO:0000114	SO:0001236	methylated_cytosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	1164879	SO:0000114	SO:0001720	methylated_cytosine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript with a translational frameshift." [SO:xp]	SO	1164880	SO:0000118	SO:0001411	transcript_with_translational_frameshift	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	SO	1164881	SO:0000120	SO:0000831	protein_coding_primary_transcript	SO:0001411
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	1164882	SO:0000121	SO:0000696	forward_primer	SO:0000695
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A folded RNA sequence." [SO:ke]	SO	1164883	SO:0000122	SO:0000001	RNA_sequence_secondary_structure	SO:0000110
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated at transcription." [SO:ma]	SO	1164884	SO:0000123	SO:0000733	transcriptionally_regulated	SO:0000400
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]	SO	1164885	SO:0000124	SO:0000401	transcriptionally_constitutive	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An inducer molecule is required for transcription to occur." [SO:ke]	SO	1164886	SO:0000125	SO:0000401	transcriptionally_induced	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A repressor molecule is required for transcription to stop." [SO:ke]	SO	1164887	SO:0000126	SO:0000401	transcriptionally_repressed	SO:0000733
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is silenced." [SO:xp]	SO	1164888	SO:0000127	SO:0000001	silenced_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is silenced by DNA modification." [SO:xp]	SO	1259837	SO:0000128	SO:0000001	gene_silenced_by_DNA_modification	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is silenced by DNA methylation." [SO:xp]	SO	1259838	SO:0000129	SO:0001411	gene_silenced_by_DNA_methylation	SO:0000001
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated after it has been translated." [SO:ke]	SO	1164892	SO:0000130	SO:0000733	post_translationally_regulated	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a gene that is regulated as it is translated." [SO:ke]	SO	1164893	SO:0000131	SO:0000733	translationally_regulated	SO:0000400
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	1164894	SO:0000132	SO:0000696	reverse_primer	SO:0000695
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]	SO	1164895	SO:0000134	SO:0000733	genomically_imprinted	SO:0000400
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	1164896	SO:0000135	SO:0000401	maternally_imprinted	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	1164897	SO:0000136	SO:0000401	paternally_imprinted	SO:0000733
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]	SO	1164898	SO:0000137	SO:0000733	allelically_excluded	SO:0000400
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	SO	1164899	SO:0000138	SO:0001411	gene_rearranged_at_DNA_level	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	1679547	SO:0000139	SO:0000233	ribosome_entry_site	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	1679548	SO:0000139	SO:0000833	ribosome_entry_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	1679549	SO:0000139	SO:0000833	ribosome_entry_site	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	1639812	SO:0000140	SO:0000831	attenuator	SO:0001411
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	1164906	SO:0000140	SO:0000673	attenuator	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1259839	SO:0000141	SO:0001411	terminator	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A folded DNA sequence." [SO:ke]	SO	1164909	SO:0000142	SO:0000001	DNA_sequence_secondary_structure	SO:0000110
4	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	1164910	SO:0000145	SO:0000316	recoded_codon	SO:0000836
5	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	1639814	SO:0000145	SO:0000836	recoded_codon	SO:0000234
5	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	1639815	SO:0000145	SO:0000836	recoded_codon	SO:0000834
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SO	1164913	SO:0000147	SO:0000831	exon	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]	SO	1679550	SO:0000147	SO:0000001	exon	SO:0000110
5	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	1259840	SO:0000148	SO:0001248	supercontig	SO:0001410
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]	SO	2452723	SO:0000149	SO:0000001	contig	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	2712710	SO:0000150	SO:0000001	read	SO:0000110
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SOFA	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	1164921	SO:0000150	SO:0000719	read	SO:0001876
5	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SOFA	sequence_assembly	SOFA	\N	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	1639820	SO:0000150	SO:0001876	read	SO:0000353
7	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]	SO	2102385	SO:0000150	SO:0001248	read	SO:0001410
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]	SO	1164924	SO:0000151	SO:0000001	clone	SO:0000110
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	1164925	SO:0000152	SO:0000695	YAC	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	1164926	SO:0000152	SO:0001411	YAC	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	1164927	SO:0000153	SO:0000695	BAC	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	1164928	SO:0000153	SO:0001411	BAC	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	1164929	SO:0000154	SO:0000695	PAC	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	1164930	SO:0000154	SO:0001411	PAC	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]	SO	1164931	SO:0000155	SO:0000001	plasmid	SO:0000110
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	1164932	SO:0000156	SO:0000695	cosmid	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	1164933	SO:0000156	SO:0001411	cosmid	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	1164934	SO:0000157	SO:0000695	phagemid	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	1164935	SO:0000157	SO:0001411	phagemid	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	1164936	SO:0000158	SO:0000695	fosmid	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	1164937	SO:0000158	SO:0001411	fosmid	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	1164938	SO:0000161	SO:0001236	methylated_adenine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	1164939	SO:0000161	SO:0001720	methylated_adenine	SO:0001411
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	1164940	SO:0000162	SO:0000673	splice_site	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	2080972	SO:0000162	SO:0001411	splice_site	SO:0000001
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1164942	SO:0000163	SO:0000835	five_prime_cis_splice_site	SO:0000185
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1164943	SO:0000163	SO:0000835	five_prime_cis_splice_site	SO:0000833
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1164944	SO:0000164	SO:0000835	three_prime_cis_splice_site	SO:0000185
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1164945	SO:0000164	SO:0000835	three_prime_cis_splice_site	SO:0000833
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164946	SO:0000165	SO:0001679	enhancer	SO:0005836
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"An enhancer bound by a factor." [SO:xp]	SO	1164947	SO:0000166	SO:0001055	enhancer_bound_by_factor	SO:0001679
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SO	1164948	SO:0000167	SO:0005836	promoter	SO:0000831
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	1164949	SO:0000169	SO:0001055	RNApol_I_promoter	SO:0001679
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	1164950	SO:0000170	SO:0001055	RNApol_II_promoter	SO:0001679
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	1164951	SO:0000171	SO:0001055	RNApol_III_promoter	SO:0001679
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164952	SO:0000172	SO:0001683	CAAT_signal	SO:0001411
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164953	SO:0000172	SO:0000167	CAAT_signal	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164954	SO:0000173	SO:0000714	GC_rich_promoter_region	SO:0001683
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164955	SO:0000173	SO:0000167	GC_rich_promoter_region	SO:0001055
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	1164956	SO:0000174	SO:0000713	TATA_box	SO:0000714
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164957	SO:0000175	SO:0001683	minus_10_signal	SO:0001411
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164958	SO:0000175	SO:0000752	minus_10_signal	SO:0001679
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164959	SO:0000175	SO:0001203	minus_10_signal	SO:0000167
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164960	SO:0000176	SO:0001683	minus_35_signal	SO:0001411
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164961	SO:0000176	SO:0000752	minus_35_signal	SO:0001679
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164962	SO:0000176	SO:0001203	minus_35_signal	SO:0000167
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A nucleotide match against a sequence from another organism." [SO:ma]	SO	1164963	SO:0000177	SO:0001410	cross_genome_match	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]	SO	1164964	SO:0000178	SO:0000001	operon	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	1259844	SO:0000179	SO:0001409	clone_insert_start	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	SO	1164967	SO:0000180	SO:0001037	retrotransposon	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	SO	1164968	SO:0000180	SO:0001037	retrotransposon	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A match against a translated sequence." [SO:ke]	SO	1164969	SO:0000181	SO:0001410	translated_nucleotide_match	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	SO	1164970	SO:0000182	SO:0001037	DNA_transposon	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	SO	1164971	SO:0000182	SO:0001037	DNA_transposon	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of the gene which is not transcribed." [SO:ke]	SO	1259845	SO:0000183	SO:0000001	non_transcribed_region	SO:0000110
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	1164974	SO:0000184	SO:0000835	U2_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	1164975	SO:0000184	SO:0000835	U2_intron	SO:0000833
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SO	1164976	SO:0000185	SO:0001411	primary_transcript	SO:0000001
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	1164977	SO:0000186	SO:0001039	LTR_retrotransposon	SO:0001037
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1164978	SO:0000188	SO:0000673	intron	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081000	SO:0000188	SO:0001411	intron	SO:0000001
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	1164980	SO:0000189	SO:0001039	non_LTR_retrotransposon	SO:0001037
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1164981	SO:0000190	SO:0000185	five_prime_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1164982	SO:0000190	SO:0000833	five_prime_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1164983	SO:0000190	SO:0000833	five_prime_intron	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1164984	SO:0000191	SO:0000185	interior_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1164985	SO:0000191	SO:0000833	interior_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1164986	SO:0000191	SO:0000833	interior_intron	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1164987	SO:0000192	SO:0000185	three_prime_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1164988	SO:0000192	SO:0000833	three_prime_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1164989	SO:0000192	SO:0000833	three_prime_intron	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]	SO	1164990	SO:0000193	SO:0001410	RFLP_fragment	SO:0000001
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	1164991	SO:0000194	SO:0000101	LINE_element	SO:0001039
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	1164992	SO:0000195	SO:0000673	coding_exon	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	2081011	SO:0000195	SO:0001411	coding_exon	SO:0000001
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	1164994	SO:0000196	SO:0000147	five_prime_coding_exon_coding_region	SO:0000833
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	1639888	SO:0000196	SO:0000833	five_prime_coding_exon_coding_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	1639889	SO:0000196	SO:0000833	five_prime_coding_exon_coding_region	SO:0001411
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	1164997	SO:0000197	SO:0000147	three_prime_coding_exon_coding_region	SO:0000833
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	1639892	SO:0000197	SO:0000833	three_prime_coding_exon_coding_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	1639893	SO:0000197	SO:0000833	three_prime_coding_exon_coding_region	SO:0001411
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"An exon that does not contain any codons." [SO:ke]	SO	1165000	SO:0000198	SO:0000673	noncoding_exon	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An exon that does not contain any codons." [SO:ke]	SO	2081016	SO:0000198	SO:0001411	noncoding_exon	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	1165002	SO:0000200	SO:0000833	five_prime_coding_exon	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	1165003	SO:0000200	SO:0000833	five_prime_coding_exon	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	1165004	SO:0000201	SO:0000673	interior_exon	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	2081019	SO:0000201	SO:0001411	interior_exon	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	1165006	SO:0000202	SO:0000833	three_prime_coding_exon	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	1165007	SO:0000202	SO:0000833	three_prime_coding_exon	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	1165008	SO:0000203	SO:0000233	UTR	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	1165009	SO:0000203	SO:0000833	UTR	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	1165010	SO:0000203	SO:0000833	UTR	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165011	SO:0000204	SO:0000234	five_prime_UTR	SO:0000233
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165012	SO:0000204	SO:0000834	five_prime_UTR	SO:0000833
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165013	SO:0000205	SO:0000234	three_prime_UTR	SO:0000233
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165014	SO:0000205	SO:0000834	three_prime_UTR	SO:0000833
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	1165015	SO:0000206	SO:0000101	SINE_element	SO:0001039
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1165016	SO:0000207	SO:0001059	simple_sequence_length_variation	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165017	SO:0000207	SO:0001411	simple_sequence_length_variation	SO:0000001
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	1165018	SO:0000208	SO:0001039	terminal_inverted_repeat_element	SO:0001037
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SO	1165019	SO:0000209	SO:0000673	rRNA_primary_transcript	SO:0000831
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	SO	1165020	SO:0000210	SO:0000673	tRNA_primary_transcript	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	1165021	SO:0000211	SO:0000185	alanine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	1165022	SO:0000212	SO:0000185	arginine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	1165023	SO:0000213	SO:0000185	asparagine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	1165024	SO:0000214	SO:0000185	aspartic_acid_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	1165025	SO:0000215	SO:0000185	cysteine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	1165026	SO:0000216	SO:0000185	glutamic_acid_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	1165027	SO:0000217	SO:0000185	glutamine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	1165028	SO:0000218	SO:0000185	glycine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	1165029	SO:0000219	SO:0000185	histidine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	1165030	SO:0000220	SO:0000185	isoleucine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	1165031	SO:0000221	SO:0000185	leucine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	1165032	SO:0000222	SO:0000185	lysine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	1165033	SO:0000223	SO:0000185	methionine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	1165034	SO:0000224	SO:0000185	phenylalanine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	1165035	SO:0000225	SO:0000185	proline_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	1165036	SO:0000226	SO:0000185	serine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	1165037	SO:0000227	SO:0000185	threonine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	1165038	SO:0000228	SO:0000185	tryptophan_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	1165039	SO:0000229	SO:0000185	tyrosine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	1165040	SO:0000230	SO:0000185	valine_tRNA_primary_transcript	SO:0000673
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	SO	1165041	SO:0000231	SO:0000673	snRNA_primary_transcript	SO:0000831
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	SO	1165042	SO:0000232	SO:0000673	snoRNA_primary_transcript	SO:0000831
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SO	1165043	SO:0000233	SO:0001411	mature_transcript	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SO	1165044	SO:0000234	SO:0000831	mRNA	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	1165045	SO:0000235	SO:0000409	TF_binding_site	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	1165046	SO:0000235	SO:0000831	TF_binding_site	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]	SO	1165047	SO:0000236	SO:0000001	ORF	SO:0000110
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	1165048	SO:0000238	SO:0001039	foldback_element	SO:0001037
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	1165049	SO:0000240	SO:0001026	chromosome_variation	SO:0001260
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	1165050	SO:0000241	SO:0000234	internal_UTR	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	1165051	SO:0000241	SO:0000834	internal_UTR	SO:0000833
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	1165052	SO:0000242	SO:0000234	untranslated_region_polycistronic_mRNA	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	1165053	SO:0000242	SO:0000834	untranslated_region_polycistronic_mRNA	SO:0000833
4	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	1165054	SO:0000243	SO:0000203	internal_ribosome_entry_site	SO:0000836
6	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	1679554	SO:0000243	SO:0000234	internal_ribosome_entry_site	SO:0000233
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	1679555	SO:0000243	SO:0000834	internal_ribosome_entry_site	SO:0000833
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]	SO	1165057	SO:0000246	SO:0000733	polyadenylated	SO:0000400
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1165058	SO:0000248	SO:0000001	sequence_length_variation	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post_transcriptionally modified base." [SO:ke]	SO	1165059	SO:0000250	SO:0000001	modified_RNA_base_feature	SO:0000110
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SO	1165060	SO:0000252	SO:0000673	rRNA	SO:0000831
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SO	1165061	SO:0000253	SO:0000673	tRNA	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	1165062	SO:0000254	SO:0000233	alanyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	1165063	SO:0000255	SO:0000185	rRNA_small_subunit_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	1165064	SO:0000256	SO:0000233	asparaginyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	1165065	SO:0000257	SO:0000233	aspartyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	1165066	SO:0000258	SO:0000233	cysteinyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	1165067	SO:0000259	SO:0000233	glutaminyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	1165068	SO:0000260	SO:0000233	glutamyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	1165069	SO:0000261	SO:0000233	glycyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	1165070	SO:0000262	SO:0000233	histidyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	1165071	SO:0000263	SO:0000233	isoleucyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	1165072	SO:0000264	SO:0000233	leucyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	1165073	SO:0000265	SO:0000233	lysyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	1165074	SO:0000266	SO:0000233	methionyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	1165075	SO:0000267	SO:0000233	phenylalanyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	1165076	SO:0000268	SO:0000233	prolyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	1165077	SO:0000269	SO:0000233	seryl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	1165078	SO:0000270	SO:0000233	threonyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	1165079	SO:0000271	SO:0000233	tryptophanyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	1165080	SO:0000272	SO:0000233	tyrosyl_tRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	1165081	SO:0000273	SO:0000233	valyl_tRNA	SO:0000673
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SO	1165082	SO:0000274	SO:0000673	snRNA	SO:0000831
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SO	1165083	SO:0000275	SO:0000673	snoRNA	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	1165084	SO:0000276	SO:0000233	miRNA	SO:0000673
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is bound by a nucleic acid." [SO:xp]	SO	1165085	SO:0000278	SO:0001411	transcript_bound_by_nucleic_acid	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is bound by a protein." [SO:xp]	SO	1165086	SO:0000279	SO:0001411	transcript_bound_by_protein	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	1165088	SO:0000281	SO:0001411	engineered_foreign_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is engineered and foreign." [SO:xp]	SO	1165090	SO:0000281	SO:0001409	engineered_foreign_gene	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	1165091	SO:0000282	SO:0000233	mRNA_with_minus_1_frameshift	SO:0000673
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	1165092	SO:0000283	SO:0001039	engineered_foreign_transposable_element_gene	SO:0001037
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	2081092	SO:0000283	SO:0001411	engineered_foreign_transposable_element_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	1165095	SO:0000283	SO:0000804	engineered_foreign_transposable_element_gene	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	\N	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	1165096	SO:0000283	SO:0000804	engineered_foreign_transposable_element_gene	SO:0001409
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	2165103	SO:0000283	SO:0000001	engineered_foreign_transposable_element_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is foreign." [SO:xp]	SO	1165098	SO:0000285	SO:0000001	foreign_gene	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2452725	SO:0000286	SO:0000001	long_terminal_repeat	SO:0000110
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165100	SO:0000286	SO:0000101	long_terminal_repeat	SO:0001039
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is a fusion." [SO:xp]	SO	1165101	SO:0000287	SO:0000001	fusion_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A fusion gene that is engineered." [SO:xp]	SO	1165102	SO:0000288	SO:0001411	engineered_fusion_gene	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A fusion gene that is engineered." [SO:xp]	SO	1639990	SO:0000288	SO:0000001	engineered_fusion_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A fusion gene that is engineered." [SO:xp]	SO	1165104	SO:0000288	SO:0001409	engineered_fusion_gene	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	SO	1165105	SO:0000289	SO:0000657	microsatellite	SO:0001411
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"" []	SO	1165106	SO:0000290	SO:0000705	dinucleotide_repeat_microsatellite_feature	SO:0000657
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"" []	SO	1165107	SO:0000291	SO:0000705	trinucleotide_repeat_microsatellite_feature	SO:0000657
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repetitive element that is engineered and foreign." [SO:xp]	SO	1165109	SO:0000293	SO:0001409	engineered_foreign_repetitive_element	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]	SO	1165110	SO:0000294	SO:0000001	inverted_repeat	SO:0000110
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	1165111	SO:0000295	SO:0000835	U12_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	1165112	SO:0000295	SO:0000835	U12_intron	SO:0000833
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1259847	SO:0000297	SO:0000001	D_loop	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165115	SO:0000299	SO:0001411	specific_recombination_site	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	1165116	SO:0000300	SO:0000298	recombination_feature_of_rearranged_gene	SO:0001411
4	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	1165117	SO:0000301	SO:0000669	vertebrate_immune_system_gene_recombination_feature	SO:0000298
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165118	SO:0000302	SO:0000300	J_gene_recombination_feature	SO:0000299
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	1165119	SO:0000303	SO:0000673	clip	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	2081103	SO:0000303	SO:0001411	clip	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165121	SO:0000305	SO:0000001	modified_DNA_base	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A nucleotide modified by methylation." [SO:ke]	SO	1165122	SO:0000306	SO:0001411	methylated_DNA_base_feature	SO:0000001
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Attribute to describe a feature that has been experimentally verified." [SO:ke]	SO	1165123	SO:0000312	SO:0000733	experimentally_determined	SO:0000400
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165124	SO:0000313	SO:0001411	stem_loop	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]	SO	1165125	SO:0000314	SO:0000001	direct_repeat	SO:0000110
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	1165126	SO:0000315	SO:0000673	TSS	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	2081104	SO:0000315	SO:0001411	TSS	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	1165128	SO:0000316	SO:0000233	CDS	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	1165129	SO:0000316	SO:0000833	CDS	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	1165130	SO:0000316	SO:0000833	CDS	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	1165131	SO:0000317	SO:0001409	cDNA_clone	SO:0000001
4	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	1165132	SO:0000318	SO:0000316	start_codon	SO:0000836
5	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	1640011	SO:0000318	SO:0000836	start_codon	SO:0000234
5	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	1640012	SO:0000318	SO:0000836	start_codon	SO:0000834
4	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	1165135	SO:0000319	SO:0000316	stop_codon	SO:0000836
5	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	1640015	SO:0000319	SO:0000836	stop_codon	SO:0000234
5	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	1640016	SO:0000319	SO:0000836	stop_codon	SO:0000834
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	1165138	SO:0000320	SO:0001679	intronic_splice_enhancer	SO:0005836
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	1165139	SO:0000320	SO:0000188	intronic_splice_enhancer	SO:0000835
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	1679556	SO:0000320	SO:0000185	intronic_splice_enhancer	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	1679557	SO:0000320	SO:0000833	intronic_splice_enhancer	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	1679558	SO:0000320	SO:0000833	intronic_splice_enhancer	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	1165143	SO:0000321	SO:0000233	mRNA_with_plus_1_frameshift	SO:0000673
4	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	SOFA	sequence	"" []	SO	1165144	SO:0000322	SO:0001654	nuclease_hypersensitive_site	SO:0000410
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	1259848	SO:0000323	SO:0000234	coding_start	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	1259849	SO:0000323	SO:0000834	coding_start	SO:0000833
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SO	1165149	SO:0000324	SO:0001409	tag	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	1165150	SO:0000325	SO:0000185	rRNA_large_subunit_primary_transcript	SO:0000673
4	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	SO	1165151	SO:0000326	SO:0000695	SAGE_tag	SO:0001409
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	1259850	SO:0000327	SO:0000234	coding_end	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	1259851	SO:0000327	SO:0000834	coding_end	SO:0000833
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"" []	SO	1165156	SO:0000328	SO:0000695	microarray_oligo	SO:0001409
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	1165157	SO:0000329	SO:0000233	mRNA_with_plus_2_frameshift	SO:0000673
4	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]	SO	1165158	SO:0000331	SO:0000695	STS	SO:0001409
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	1165159	SO:0000332	SO:0000001	coding_conserved_region	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	1165160	SO:0000333	SO:0000831	exon_junction	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]	SO	1165161	SO:0000334	SO:0000001	nc_conserved_region	SO:0000110
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	1165162	SO:0000335	SO:0000233	mRNA_with_minus_2_frameshift	SO:0000673
4	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]	SO	1165163	SO:0000337	SO:0000695	RNAi_reagent	SO:0001409
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	1165164	SO:0000338	SO:0000101	MITE	SO:0001039
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region in a genome which promotes recombination." [SO:rd]	SO	1165165	SO:0000339	SO:0000001	recombination_hotspot	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	SO	1165166	SO:0000340	SO:0000001	chromosome	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SO	1165167	SO:0000341	SO:0001235	chromosome_band	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]	SO	1679559	SO:0000341	SO:0000001	chromosome_band	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	1165169	SO:0000342	SO:0000298	site_specific_recombination_target_region	SO:0001411
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Region of a transcript that regulates splicing." [SO:ke]	SO	1165170	SO:0000344	SO:0005836	splice_enhancer	SO:0000831
4	"A region which is intended for use in an experiment." [SO:cb]	SOFA	biomaterial_region	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	SO	1165171	SO:0000345	SO:0000695	EST	SO:0001409
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1165172	SO:0000346	SO:0000299	loxP_site	SO:0000669
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A match against a nucleotide sequence." [SO:ke]	SO	1165173	SO:0000347	SO:0000001	nucleotide_match	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A match against a protein sequence." [SO:ke]	SO	1165174	SO:0000349	SO:0000001	protein_match	SO:0000110
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	1165175	SO:0000350	SO:0000299	FRT_site	SO:0000669
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	SO	1165176	SO:0000353	SO:0000001	sequence_assembly	SO:0000110
4	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	SOFA	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	1165177	SO:0000354	SO:0001654	group_1_intron_homing_endonuclease_target_region	SO:0000410
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]	SO	1165178	SO:0000355	SO:0000001	haplotype_block	SO:0000110
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	1259852	SO:0000360	SO:0000234	codon	SO:0000233
5	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	1259853	SO:0000360	SO:0000834	codon	SO:0000833
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]	SO	1165183	SO:0000362	SO:0000733	invalidated_by_chimeric_cDNA	SO:0000400
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transgene that is floxed." [SO:xp]	SO	1165184	SO:0000363	SO:0001411	floxed_gene	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of sequence surrounding a transposable element." [SO:ke]	SO	1165185	SO:0000364	SO:0000001	transposable_element_flanking_region	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	SO	1640053	SO:0000365	SO:0000001	integron	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]	SO	1165187	SO:0000365	SO:0001411	integron	SO:0000001
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	1165188	SO:0000367	SO:0000299	attI_site	SO:0000669
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	1165189	SO:0000367	SO:0001037	attI_site	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	1165190	SO:0000367	SO:0001037	attI_site	SO:0001411
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SO	1165191	SO:0000370	SO:0000673	small_regulatory_ncRNA	SO:0000831
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	1165192	SO:0000371	SO:0001039	conjugative_transposon	SO:0001037
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	1165193	SO:0000372	SO:0001411	enzymatic_RNA	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recombinationally rearranged gene by inversion." [SO:xp]	SO	1165194	SO:0000373	SO:0001411	recombinationally_inverted_gene	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An RNA with catalytic activity." [SO:ma]	SO	1165195	SO:0000374	SO:0000831	ribozyme	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	1165196	SO:0000375	SO:0000655	rRNA_5_8S	SO:0000233
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	1165197	SO:0000376	SO:0000233	RNA_6S	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	1165198	SO:0000377	SO:0000233	CsrB_RsmB_RNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	1165199	SO:0000378	SO:0000233	DsrA_RNA	SO:0000673
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	1165200	SO:0000379	SO:0000655	GcvB_RNA	SO:0000233
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]	SO	1165201	SO:0000380	SO:0001683	hammerhead_ribozyme	SO:0001411
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"" []	SO	1165202	SO:0000381	SO:0000188	group_IIA_intron	SO:0000835
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"" []	SO	1165203	SO:0000382	SO:0000188	group_IIB_intron	SO:0000835
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	1165204	SO:0000383	SO:0000233	MicF_RNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	1165205	SO:0000384	SO:0000233	OxyS_RNA	SO:0000673
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SO	1165206	SO:0000385	SO:0000673	RNase_MRP_RNA	SO:0000831
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SO	1165207	SO:0000386	SO:0000673	RNase_P_RNA	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	1165208	SO:0000387	SO:0000233	RprA_RNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	1165209	SO:0000388	SO:0000233	RRE_RNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	1165210	SO:0000389	SO:0000233	spot_42_RNA	SO:0000673
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SO	1165211	SO:0000390	SO:0000673	telomerase_RNA	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	1165212	SO:0000391	SO:0000233	U1_snRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	1165213	SO:0000392	SO:0000233	U2_snRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	1165214	SO:0000393	SO:0000233	U4_snRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	1165215	SO:0000394	SO:0000233	U4atac_snRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	1165216	SO:0000395	SO:0000233	U5_snRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	1165217	SO:0000396	SO:0000233	U6_snRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	1165218	SO:0000397	SO:0000233	U6atac_snRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	1165219	SO:0000398	SO:0000233	U11_snRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	1165220	SO:0000399	SO:0000233	U12_snRNA	SO:0000673
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	1165221	SO:0000403	SO:0000655	U14_snoRNA	SO:0000233
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SO	1165222	SO:0000404	SO:0000673	vault_RNA	SO:0000831
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SO	1165223	SO:0000405	SO:0000673	Y_RNA	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	1165224	SO:0000406	SO:0000185	twintron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	1165225	SO:0000406	SO:0000833	twintron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	1165226	SO:0000406	SO:0000833	twintron	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	1165227	SO:0000407	SO:0000655	rRNA_18S	SO:0000233
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	SO	1165228	SO:0000410	SO:0000001	protein_binding_site	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region that rescues." [SO:xp]	SO	1165229	SO:0000411	SO:0000001	rescue_region	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]	SO	1165230	SO:0000412	SO:0000001	restriction_fragment	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region where the sequence differs from that of a specified sequence." [SO:ke]	SO	1165231	SO:0000413	SO:0000001	sequence_difference	SO:0000110
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]	SO	1165232	SO:0000414	SO:0000733	invalidated_by_genomic_contamination	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]	SO	1165233	SO:0000415	SO:0000733	invalidated_by_genomic_polyA_primed_cDNA	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]	SO	1165234	SO:0000416	SO:0000733	invalidated_by_partial_processing	SO:0000400
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	1165235	SO:0000417	SO:0000104	polypeptide_domain	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	1640096	SO:0000417	SO:0001411	polypeptide_domain	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1679560	SO:0000418	SO:0000104	signal_peptide	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens,SOFA	region	SOFA	SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2165108	SO:0000418	SO:0001411	signal_peptide	SO:0000001
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens,SOFA	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165241	SO:0000418	SO:0001063	signal_peptide	SO:0000839
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens,SOFA	sequence_feature	SOFA	SOFA	sequence	"The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]	SO	1679562	SO:0000419	SO:0000001	mature_protein_region	SO:0000110
4	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1165243	SO:0000420	SO:0000182	five_prime_terminal_inverted_repeat	SO:0000101
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165244	SO:0000420	SO:0000657	five_prime_terminal_inverted_repeat	SO:0001411
4	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1165245	SO:0000421	SO:0000182	three_prime_terminal_inverted_repeat	SO:0000101
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165246	SO:0000421	SO:0000657	three_prime_terminal_inverted_repeat	SO:0001411
4	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1165247	SO:0000422	SO:0000186	U5_LTR_region	SO:0000180
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165248	SO:0000422	SO:0000657	U5_LTR_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165249	SO:0000422	SO:0001412	U5_LTR_region	SO:0000001
4	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1165250	SO:0000423	SO:0000186	R_LTR_region	SO:0000180
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165251	SO:0000423	SO:0000657	R_LTR_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165252	SO:0000423	SO:0001412	R_LTR_region	SO:0000001
4	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1165253	SO:0000424	SO:0000186	U3_LTR_region	SO:0000180
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165254	SO:0000424	SO:0000657	U3_LTR_region	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165255	SO:0000424	SO:0001412	U3_LTR_region	SO:0000001
4	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1165256	SO:0000425	SO:0000180	five_prime_LTR	SO:0000101
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706577	SO:0000425	SO:0001411	five_prime_LTR	SO:0000001
4	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1165258	SO:0000426	SO:0000180	three_prime_LTR	SO:0000101
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706579	SO:0000426	SO:0001411	three_prime_LTR	SO:0000001
4	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	1165260	SO:0000427	SO:0000286	R_five_prime_LTR_region	SO:0000186
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	1165261	SO:0000427	SO:0000286	R_five_prime_LTR_region	SO:0000657
4	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	1165262	SO:0000427	SO:0000840	R_five_prime_LTR_region	SO:0001412
4	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	1165263	SO:0000428	SO:0000286	U5_five_prime_LTR_region	SO:0000186
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	1165264	SO:0000428	SO:0000286	U5_five_prime_LTR_region	SO:0000657
4	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	1165265	SO:0000428	SO:0000840	U5_five_prime_LTR_region	SO:0001412
4	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	1165266	SO:0000429	SO:0000286	U3_five_prime_LTR_region	SO:0000186
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	1165267	SO:0000429	SO:0000286	U3_five_prime_LTR_region	SO:0000657
4	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	1165268	SO:0000429	SO:0000840	U3_five_prime_LTR_region	SO:0001412
4	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	1165269	SO:0000430	SO:0000286	R_three_prime_LTR_region	SO:0000186
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	1165270	SO:0000430	SO:0000286	R_three_prime_LTR_region	SO:0000657
4	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	1165271	SO:0000430	SO:0000840	R_three_prime_LTR_region	SO:0001412
4	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	1165272	SO:0000431	SO:0000286	U3_three_prime_LTR_region	SO:0000186
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	1165273	SO:0000431	SO:0000286	U3_three_prime_LTR_region	SO:0000657
4	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	1165274	SO:0000431	SO:0000840	U3_three_prime_LTR_region	SO:0001412
4	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	\N	LTR_retrotransposon	\N	\N	sequence	"" []	SO	1165275	SO:0000432	SO:0000286	U5_three_prime_LTR_region	SO:0000186
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	\N	sequence	"" []	SO	1165276	SO:0000432	SO:0000286	U5_three_prime_LTR_region	SO:0000657
4	"A region that is defined according to its relations with other regions within the same sequence." [SO:cb]	\N	topologically_defined_region	SOFA	\N	sequence	"" []	SO	1165277	SO:0000432	SO:0000840	U5_three_prime_LTR_region	SO:0001412
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	2452726	SO:0000433	SO:0000001	non_LTR_retrotransposon_polymeric_tract	SO:0000110
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	1165279	SO:0000433	SO:0000101	non_LTR_retrotransposon_polymeric_tract	SO:0001039
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]	SO	1165280	SO:0000434	SO:0001411	target_site_duplication	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	2706586	SO:0000435	SO:0000001	RR_tract	SO:0000110
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	1165282	SO:0000435	SO:0000101	RR_tract	SO:0001039
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]	SO	1259858	SO:0000436	SO:0000001	ARS	SO:0000110
4	"" []	\N	chromosome_variation	\N	\N	sequence	"" []	SO	1165285	SO:0000439	SO:1000183	inverted_ring_chromosome	SO:0000240
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	1640141	SO:0000440	SO:0000001	vector_replicon	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]	SO	1165287	SO:0000440	SO:0001409	vector_replicon	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A single stranded oligonucleotide." [SO:ke]	SO	1165288	SO:0000441	SO:0001409	ss_oligo	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A double stranded oligonucleotide." [SO:ke]	SO	1165289	SO:0000442	SO:0001409	ds_oligo	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	1165290	SO:0000444	SO:0000833	three_prime_noncoding_exon	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	1165291	SO:0000444	SO:0000833	three_prime_noncoding_exon	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	1165292	SO:0000445	SO:0000833	five_prime_noncoding_exon	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	1165293	SO:0000445	SO:0000833	five_prime_noncoding_exon	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	1165294	SO:0000446	SO:0000185	UTR_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	1165295	SO:0000446	SO:0000833	UTR_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	1165296	SO:0000446	SO:0000833	UTR_intron	SO:0001411
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	1165297	SO:0000447	SO:0000835	five_prime_UTR_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	1165298	SO:0000447	SO:0000835	five_prime_UTR_intron	SO:0000833
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	1165299	SO:0000448	SO:0000835	three_prime_UTR_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	1165300	SO:0000448	SO:0000835	three_prime_UTR_intron	SO:0000833
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	SO	1165301	SO:0000450	SO:0001235	interband	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A light region between two darkly staining bands in a polytene chromosome." [SO:ma]	SO	1679563	SO:0000450	SO:0000001	interband	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes a polyadenylated mRNA." [SO:xp]	SO	1165303	SO:0000451	SO:0001411	gene_with_polyadenylated_mRNA	SO:0000001
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	1165304	SO:0000453	SO:0001507	chromosomal_transposition	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	1165305	SO:0000453	SO:0001524	chromosomal_transposition	SO:0001506
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SO	1165306	SO:0000454	SO:0000673	rasiRNA	SO:0000831
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes an mRNA with a frameshift." [SO:xp]	SO	1165307	SO:0000455	SO:0001411	gene_with_mRNA_with_frameshift	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is recombinationally rearranged." [SO:ke]	SO	1165308	SO:0000456	SO:0000001	recombinationally_rearranged_gene	SO:0000110
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	1165309	SO:0000457	SO:0000240	interchromosomal_duplication	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	1165310	SO:0000457	SO:0000240	interchromosomal_duplication	SO:0001524
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165311	SO:0000458	SO:0000300	D_gene_segment	SO:0000299
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene with a transcript that is trans-spliced." [SO:xp]	SO	1165312	SO:0000459	SO:0000001	gene_with_trans_spliced_transcript	SO:0000110
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1165313	SO:0000460	SO:0000299	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000669
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	1165314	SO:0000461	SO:1000183	inversion_derived_bipartite_deficiency	SO:0000240
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A non-functional descendant of an exon." [SO:ke]	SO	1165315	SO:0000464	SO:0000001	decayed_exon	SO:0000110
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	1165316	SO:0000465	SO:1000183	inversion_derived_deficiency_plus_duplication	SO:0000240
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165317	SO:0000466	SO:0000300	V_gene_segment	SO:0000299
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]	SO	1165318	SO:0000467	SO:0000401	post_translationally_regulated_by_protein_stability	SO:0000733
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	1679564	SO:0000468	SO:0000001	golden_path_fragment	SO:0000110
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"One of the pieces of sequence that make up a golden path." [SO:rd]	SO	1165320	SO:0000468	SO:0001248	golden_path_fragment	SO:0001410
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]	SO	1165321	SO:0000469	SO:0000401	post_translationally_regulated_by_protein_modification	SO:0000733
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165322	SO:0000470	SO:0000300	J_gene_segment	SO:0000299
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation." [SO:ke]	SO	1165323	SO:0000471	SO:0000401	autoregulated	SO:0000733
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	SO	1165324	SO:0000472	SO:0001410	tiling_path	SO:0000001
4	"" []	\N	gene_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	1165325	SO:0000473	SO:0000119	negatively_autoregulated	SO:0000401
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	1679565	SO:0000474	SO:0000001	tiling_path_fragment	SO:0000110
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]	SO	1165327	SO:0000474	SO:0001248	tiling_path_fragment	SO:0001410
4	"" []	\N	gene_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	1165328	SO:0000475	SO:0000119	positively_autoregulated	SO:0000401
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	2764352	SO:0000476	SO:0001410	contig_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	1165331	SO:0000476	SO:0000148	contig_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	1165332	SO:0000476	SO:0000148	contig_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	2279384	SO:0000476	SO:0000353	contig_read	SO:0001248
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165334	SO:0000478	SO:0000300	C_gene_segment	SO:0000299
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is trans-spliced." [SO:xp]	SO	1165335	SO:0000479	SO:0001411	trans_spliced_transcript	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	1165336	SO:0000480	SO:0001409	tiling_path_clone	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	2081243	SO:0000480	SO:0001410	tiling_path_clone	SO:0000001
4	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	1165338	SO:0000480	SO:0000353	tiling_path_clone	SO:0001248
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	2441246	SO:0000481	SO:0001411	terminal_inverted_repeat	SO:0000001
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	1165340	SO:0000481	SO:0000101	terminal_inverted_repeat	SO:0001039
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1165341	SO:0000482	SO:0000299	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000669
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A primary transcript that is never translated into a protein." [SO:ke]	SO	1165342	SO:0000483	SO:0000831	nc_primary_transcript	SO:0001411
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	1165343	SO:0000484	SO:0000147	three_prime_coding_exon_noncoding_region	SO:0000833
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	1640191	SO:0000484	SO:0000833	three_prime_coding_exon_noncoding_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	1640192	SO:0000484	SO:0000833	three_prime_coding_exon_noncoding_region	SO:0001411
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165346	SO:0000485	SO:0000300	DJ_J_cluster	SO:0000299
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	1165347	SO:0000486	SO:0000147	five_prime_coding_exon_noncoding_region	SO:0000833
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	1640196	SO:0000486	SO:0000833	five_prime_coding_exon_noncoding_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	1640197	SO:0000486	SO:0000833	five_prime_coding_exon_noncoding_region	SO:0001411
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165350	SO:0000487	SO:0000300	VDJ_J_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165351	SO:0000488	SO:0000300	VDJ_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165352	SO:0000489	SO:0000300	VJ_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165353	SO:0000490	SO:0000300	VJ_J_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165354	SO:0000491	SO:0000300	VJ_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	1165355	SO:0000492	SO:0000300	D_gene_recombination_feature	SO:0000299
5	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1259860	SO:0000493	SO:0000301	three_prime_D_heptamer	SO:0000300
5	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1259861	SO:0000494	SO:0000301	three_prime_D_nonamer	SO:0000300
6	"" []	\N	specific_recombination_site	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1679566	SO:0000495	SO:0000300	three_prime_D_spacer	SO:0000299
4	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165361	SO:0000495	SO:0000939	three_prime_D_spacer	SO:0000301
5	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1259862	SO:0000496	SO:0000301	five_prime_D_heptamer	SO:0000300
5	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1259863	SO:0000497	SO:0000301	five_prime_D_nonamer	SO:0000300
6	"" []	\N	specific_recombination_site	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1679567	SO:0000498	SO:0000300	five_prime_D_spacer	SO:0000299
4	"" []	\N	vertebrate_immune_system_gene_recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165367	SO:0000498	SO:0000939	five_prime_D_spacer	SO:0000301
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]	SO	1165368	SO:0000499	SO:0001410	virtual_sequence	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]	SO	1165369	SO:0000500	SO:0001411	Hoogsteen_base_pair	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A type of non-canonical base-pairing." [SO:ke]	SO	1165370	SO:0000501	SO:0001411	reverse_Hoogsteen_base_pair	SO:0000001
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165371	SO:0000504	SO:0000300	D_DJ_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165372	SO:0000505	SO:0000300	D_DJ_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165373	SO:0000506	SO:0000300	D_DJ_J_C_cluster	SO:0000299
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non functional descendant of an exon, part of a pseudogene." [SO:ke]	SO	1259864	SO:0000507	SO:0000001	pseudogenic_exon	SO:0000110
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165375	SO:0000508	SO:0000300	D_DJ_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165376	SO:0000509	SO:0000300	D_J_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165377	SO:0000510	SO:0000300	VD_gene_segment	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165378	SO:0000511	SO:0000300	J_C_cluster	SO:0000299
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	1165379	SO:0000512	SO:1000183	inversion_derived_deficiency_plus_aneuploid	SO:0000240
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165380	SO:0000513	SO:0000300	J_cluster	SO:0000299
4	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165381	SO:0000514	SO:0000301	J_nonamer	SO:0000300
4	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165382	SO:0000515	SO:0000301	J_heptamer	SO:0000300
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non functional descendant of a transcript, part of a pseudogene." [SO:ke]	SO	1165383	SO:0000516	SO:0000001	pseudogenic_transcript	SO:0000110
5	"" []	\N	specific_recombination_site	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1259865	SO:0000517	SO:0000300	J_spacer	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165386	SO:0000518	SO:0000300	V_DJ_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165387	SO:0000519	SO:0000300	V_DJ_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165388	SO:0000520	SO:0000300	V_VDJ_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165389	SO:0000521	SO:0000300	V_VDJ_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165390	SO:0000522	SO:0000300	V_VDJ_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165391	SO:0000523	SO:0000300	V_VJ_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165392	SO:0000524	SO:0000300	V_VJ_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165393	SO:0000525	SO:0000300	V_VJ_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165394	SO:0000526	SO:0000300	V_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165395	SO:0000527	SO:0000300	V_D_DJ_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165396	SO:0000528	SO:0000300	V_D_DJ_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165397	SO:0000529	SO:0000300	V_D_DJ_J_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165398	SO:0000530	SO:0000300	V_D_DJ_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165399	SO:0000531	SO:0000300	V_D_J_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165400	SO:0000532	SO:0000300	V_D_J_cluster	SO:0000299
4	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165401	SO:0000533	SO:0000301	V_heptamer	SO:0000300
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165402	SO:0000534	SO:0000300	V_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165403	SO:0000535	SO:0000300	V_J_C_cluster	SO:0000299
4	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165404	SO:0000536	SO:0000301	V_nonamer	SO:0000300
5	"" []	\N	specific_recombination_site	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1259866	SO:0000537	SO:0000300	V_spacer	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165407	SO:0000538	SO:0000300	V_gene_recombination_feature	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165408	SO:0000539	SO:0000300	DJ_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165409	SO:0000540	SO:0000300	DJ_J_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165410	SO:0000541	SO:0000300	VDJ_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165411	SO:0000542	SO:0000300	V_DJ_C_cluster	SO:0000299
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	1165412	SO:0000544	SO:0001039	helitron	SO:0001037
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	2706648	SO:0000545	SO:0001411	recoding_pseudoknot	SO:0000001
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	1165414	SO:0000545	SO:0000234	recoding_pseudoknot	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	1165415	SO:0000545	SO:0000834	recoding_pseudoknot	SO:0000833
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	1165416	SO:0000547	SO:1000183	inversion_derived_bipartite_duplication	SO:0000240
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes a transcript that is edited." [SO:xp]	SO	1165417	SO:0000548	SO:0001411	gene_with_edited_transcript	SO:0000001
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	1165418	SO:0000549	SO:1000183	inversion_derived_duplication_plus_aneuploid	SO:0000240
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	1165419	SO:0000550	SO:0001507	aneuploid_chromosome	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	1165420	SO:0000550	SO:0001524	aneuploid_chromosome	SO:0001506
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165421	SO:0000551	SO:0000831	polyA_signal_sequence	SO:0001411
4	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	1165422	SO:0000552	SO:0000203	Shine_Dalgarno_sequence	SO:0000836
6	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	1679568	SO:0000552	SO:0000234	Shine_Dalgarno_sequence	SO:0000233
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	1679569	SO:0000552	SO:0000834	Shine_Dalgarno_sequence	SO:0000833
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SOFA	mRNA	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165425	SO:0000553	SO:0000836	polyA_site	SO:0000234
4	"A region of a mature transcript." [SO:ke]	SOFA	mature_transcript_region	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165426	SO:0000553	SO:0000836	polyA_site	SO:0000834
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2452727	SO:0000553	SO:0000831	polyA_site	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165428	SO:0000555	SO:0000185	five_prime_clip	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165429	SO:0000555	SO:0000833	five_prime_clip	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165430	SO:0000555	SO:0000833	five_prime_clip	SO:0001411
4	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165431	SO:0000556	SO:0000301	five_prime_D_recombination_signal_sequence	SO:0000300
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165432	SO:0000557	SO:0000185	three_prime_clip	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165433	SO:0000557	SO:0000833	three_prime_clip	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165434	SO:0000557	SO:0000833	three_prime_clip	SO:0001411
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165435	SO:0000558	SO:0000300	C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165436	SO:0000559	SO:0000300	D_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165437	SO:0000560	SO:0000300	D_J_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165438	SO:0000561	SO:0000300	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"" []	SO	1165439	SO:0000562	SO:0000300	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000299
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1165440	SO:0000563	SO:0000299	vertebrate_immune_system_gene_recombination_spacer	SO:0000669
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165441	SO:0000564	SO:0000300	V_DJ_J_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165442	SO:0000565	SO:0000300	V_VDJ_J_C_cluster	SO:0000299
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165443	SO:0000566	SO:0000300	V_VJ_J_C_cluster	SO:0000299
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	1165444	SO:0000567	SO:0000240	inversion_derived_aneuploid_chromosome	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	1165445	SO:0000567	SO:0000240	inversion_derived_aneuploid_chromosome	SO:0001524
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	1165446	SO:0000568	SO:0001679	bidirectional_promoter	SO:0005836
4	"" []	\N	recombination_feature_of_rearranged_gene	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165447	SO:0000570	SO:0000301	three_prime_D_recombination_signal_sequence	SO:0000300
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165448	SO:0000571	SO:0000733	miRNA_encoding	SO:0000400
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165449	SO:0000572	SO:0000300	DJ_gene_segment	SO:0000299
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165450	SO:0000573	SO:0000733	rRNA_encoding	SO:0000400
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165451	SO:0000574	SO:0000300	VDJ_gene_segment	SO:0000299
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165452	SO:0000575	SO:0000733	scRNA_encoding	SO:0000400
4	"" []	\N	specific_recombination_site	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1165453	SO:0000576	SO:0000300	VJ_gene_segment	SO:0000299
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	1165454	SO:0000577	SO:0000340	centromere	SO:0001235
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	2081339	SO:0000577	SO:0001411	centromere	SO:0000001
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165456	SO:0000578	SO:0000733	snoRNA_encoding	SO:0000400
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A locatable feature on a transcript that is edited." [SO:ma]	SO	1165457	SO:0000579	SO:0000831	edited_transcript_feature	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A locatable feature on a transcript that is edited." [SO:ma]	SO	1679570	SO:0000579	SO:0000001	edited_transcript_feature	SO:0000110
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	1165459	SO:0000580	SO:0000185	methylation_guide_snoRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	1165460	SO:0000582	SO:0000185	rRNA_cleavage_snoRNA_primary_transcript	SO:0000673
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	1165461	SO:0000583	SO:0000673	pre_edited_region	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	2081342	SO:0000583	SO:0001411	pre_edited_region	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	1165463	SO:0000584	SO:0000233	tmRNA	SO:0000673
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	1165464	SO:0000585	SO:0000401	C_D_box_snoRNA_encoding	SO:0000733
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	SO	1165465	SO:0000586	SO:0000673	tmRNA_primary_transcript	SO:0000831
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	1165466	SO:0000587	SO:0000835	group_I_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	1165467	SO:0000587	SO:0000835	group_I_intron	SO:0000833
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	1165468	SO:0000588	SO:0000185	autocatalytically_spliced_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	1165469	SO:0000588	SO:0000833	autocatalytically_spliced_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	1165470	SO:0000588	SO:0000833	autocatalytically_spliced_intron	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	SO	1165471	SO:0000589	SO:0000673	SRP_RNA_primary_transcript	SO:0000831
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SO	1165472	SO:0000590	SO:0000673	SRP_RNA	SO:0000831
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]	SO	1165473	SO:0000591	SO:0000001	pseudoknot	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]	SO	1165474	SO:0000592	SO:0001411	H_pseudoknot	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	1165475	SO:0000593	SO:0000233	C_D_box_snoRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	1165476	SO:0000594	SO:0000233	H_ACA_box_snoRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	1165477	SO:0000595	SO:0000185	C_D_box_snoRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	1165478	SO:0000596	SO:0000185	H_ACA_box_snoRNA_primary_transcript	SO:0000673
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SO	1165479	SO:0000602	SO:0000673	guide_RNA	SO:0000831
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	1165480	SO:0000603	SO:0000835	group_II_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	1165481	SO:0000603	SO:0000835	group_II_intron	SO:0000833
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	1165482	SO:0000604	SO:0000673	editing_block	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	2081358	SO:0000604	SO:0001411	editing_block	SO:0000001
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	1165484	SO:0000606	SO:0000673	editing_domain	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	2081359	SO:0000606	SO:0001411	editing_domain	SO:0000001
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	1165486	SO:0000607	SO:0000673	unedited_region	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	2081360	SO:0000607	SO:0001411	unedited_region	SO:0000001
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	1165488	SO:0000608	SO:0000401	H_ACA_box_snoRNA_encoding	SO:0000733
4	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	1165489	SO:0000611	SO:0000188	branch_site	SO:0000835
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	1679571	SO:0000611	SO:0000185	branch_site	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	1679572	SO:0000611	SO:0000833	branch_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	1679573	SO:0000611	SO:0000833	branch_site	SO:0001411
4	"A part of a primary transcript." [SO:ke]	SOFA	primary_transcript_region	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	1165493	SO:0000612	SO:0000188	polypyrimidine_tract	SO:0000835
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	1679574	SO:0000612	SO:0000185	polypyrimidine_tract	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	1679575	SO:0000612	SO:0000833	polypyrimidine_tract	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	1679576	SO:0000612	SO:0000833	polypyrimidine_tract	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	1679577	SO:0000613	SO:0005836	bacterial_RNApol_promoter	SO:0000831
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	1165498	SO:0000613	SO:0001055	bacterial_RNApol_promoter	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	1640341	SO:0000614	SO:0000831	bacterial_terminator	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	1165500	SO:0000614	SO:0005836	bacterial_terminator	SO:0000831
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	1165501	SO:0000615	SO:0000673	terminator_of_type_2_RNApol_III_promoter	SO:0000831
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	1165502	SO:0000615	SO:0001679	terminator_of_type_2_RNApol_III_promoter	SO:0005836
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	1165503	SO:0000616	SO:0000673	transcription_end_site	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	2081369	SO:0000616	SO:0001411	transcription_end_site	SO:0000001
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1165505	SO:0000617	SO:0000167	RNApol_III_promoter_type_1	SO:0001055
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1165506	SO:0000618	SO:0000167	RNApol_III_promoter_type_2	SO:0001055
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	1165507	SO:0000619	SO:0000713	A_box	SO:0000714
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	1165508	SO:0000620	SO:0000713	B_box	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	1165509	SO:0000620	SO:0001203	B_box	SO:0000167
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1165510	SO:0000621	SO:0000167	RNApol_III_promoter_type_3	SO:0001055
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	1165511	SO:0000622	SO:0000713	C_box	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	1165512	SO:0000622	SO:0001203	C_box	SO:0000167
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165513	SO:0000623	SO:0000733	snRNA_encoding	SO:0000400
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	SOFA	replicon	SOFA	SOFA	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	1165514	SO:0000624	SO:0000340	telomere	SO:0001235
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	2081378	SO:0000624	SO:0001411	telomere	SO:0000001
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SOFA	regulatory_region	SOFA	SOFA	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	1165516	SO:0000625	SO:0001679	silencer	SO:0005836
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165517	SO:0000626	SO:0001235	chromosomal_regulatory_element	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1679578	SO:0000626	SO:0000001	chromosomal_regulatory_element	SO:0000110
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SO	1165519	SO:0000627	SO:0005836	insulator	SO:0000831
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"" []	SO	1165520	SO:0000628	SO:0001235	chromosomal_structural_element	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1679579	SO:0000628	SO:0000001	chromosomal_structural_element	SO:0000110
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1679580	SO:0000629	SO:0000233	five_prime_open_reading_frame	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1679581	SO:0000629	SO:0000833	five_prime_open_reading_frame	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1679582	SO:0000629	SO:0000833	five_prime_open_reading_frame	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	1165527	SO:0000630	SO:0000234	upstream_AUG_codon	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	1165528	SO:0000630	SO:0000834	upstream_AUG_codon	SO:0000833
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	1165529	SO:0000631	SO:0000831	polycistronic_primary_transcript	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	1165530	SO:0000632	SO:0000831	monocistronic_primary_transcript	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	1259867	SO:0000633	SO:0000831	monocistronic_mRNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	1259868	SO:0000634	SO:0000831	polycistronic_mRNA	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	SO	1165535	SO:0000635	SO:0000831	mini_exon_donor_RNA	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1165536	SO:0000636	SO:0000673	spliced_leader_RNA	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2081390	SO:0000636	SO:0001411	spliced_leader_RNA	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid that is engineered." [SO:xp]	SO	1165538	SO:0000637	SO:0001411	engineered_plasmid	SO:0000001
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	1165540	SO:0000638	SO:0000483	transcribed_spacer_region	SO:0000185
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	1640373	SO:0000638	SO:0000185	transcribed_spacer_region	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	1165542	SO:0000638	SO:0000833	transcribed_spacer_region	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	1165543	SO:0000638	SO:0000833	transcribed_spacer_region	SO:0001411
4	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	1165544	SO:0000639	SO:0000209	internal_transcribed_spacer_region	SO:0000483
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	1165545	SO:0000639	SO:0000835	internal_transcribed_spacer_region	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	1165546	SO:0000639	SO:0000835	internal_transcribed_spacer_region	SO:0000833
4	"A primary transcript that is never translated into a protein." [SO:ke]	\N	nc_primary_transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	1165547	SO:0000640	SO:0000209	external_transcribed_spacer_region	SO:0000483
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	1165548	SO:0000640	SO:0000835	external_transcribed_spacer_region	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	1165549	SO:0000640	SO:0000835	external_transcribed_spacer_region	SO:0000833
4	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"" []	SO	1165550	SO:0000641	SO:0000705	tetranucleotide_repeat_microsatellite_feature	SO:0000657
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165551	SO:0000642	SO:0000733	SRP_RNA_encoding	SO:0000400
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]	SO	1165552	SO:0000643	SO:0000657	minisatellite	SO:0001411
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SO	1165553	SO:0000644	SO:0000673	antisense_RNA	SO:0000831
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The reverse complement of the primary transcript." [SO:ke]	SO	1165554	SO:0000645	SO:0000831	antisense_primary_transcript	SO:0001411
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SO	1165555	SO:0000646	SO:0000673	siRNA	SO:0000831
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a micro RNA." [SO:ke]	SO	1165556	SO:0000647	SO:0000673	miRNA_primary_transcript	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	1165557	SO:0000648	SO:0000185	stRNA_primary_transcript	SO:0000673
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SO	1165558	SO:0000649	SO:0000673	stRNA	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	1165559	SO:0000650	SO:0000233	small_subunit_rRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	1165560	SO:0000651	SO:0000233	large_subunit_rRNA	SO:0000673
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	1165561	SO:0000652	SO:0000655	rRNA_5S	SO:0000233
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	1165562	SO:0000653	SO:0000655	rRNA_28S	SO:0000233
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	1165563	SO:0000654	SO:0000704	maxicircle_gene	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	1640396	SO:0000654	SO:0001411	maxicircle_gene	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SO	1165565	SO:0000655	SO:0000831	ncRNA	SO:0001411
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165566	SO:0000656	SO:0000733	stRNA_encoding	SO:0000400
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A repeat that is located at dispersed sites in the genome." [SO:ke]	SO	1165567	SO:0000658	SO:0000001	dispersed_repeat	SO:0000110
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165568	SO:0000659	SO:0000733	tmRNA_encoding	SO:0000400
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	1165569	SO:0000662	SO:0000185	spliceosomal_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	1165570	SO:0000662	SO:0000833	spliceosomal_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	1165571	SO:0000662	SO:0000833	spliceosomal_intron	SO:0001411
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165572	SO:0000663	SO:0000733	tRNA_encoding	SO:0000400
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165573	SO:0000664	SO:0001235	introgressed_chromosome_region	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1679583	SO:0000664	SO:0000001	introgressed_chromosome_region	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is monocistronic." [SO:xp]	SO	1165575	SO:0000665	SO:0001411	monocistronic_transcript	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	1165576	SO:0000666	SO:0000185	mobile_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	1165577	SO:0000666	SO:0000833	mobile_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	1165578	SO:0000666	SO:0000833	mobile_intron	SO:0001411
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A match against an EST sequence." [SO:ke]	SO	1165580	SO:0000668	SO:0000343	EST_match	SO:0001410
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1165581	SO:0000669	SO:0000001	sequence_rearrangement_feature	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]	SO	1165582	SO:0000670	SO:0001411	chromosome_breakage_sequence	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]	SO	1165583	SO:0000671	SO:0001411	internal_eliminated_sequence	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]	SO	1165584	SO:0000672	SO:0001411	macronucleus_destined_segment	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SO	1165585	SO:0000673	SO:0000001	transcript	SO:0000110
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	1165586	SO:0000676	SO:0000162	canonical_three_prime_splice_site	SO:0000835
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	1165587	SO:0000677	SO:0000162	canonical_five_prime_splice_site	SO:0000835
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	1165588	SO:0000678	SO:0000162	non_canonical_three_prime_splice_site	SO:0000835
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	1165589	SO:0000679	SO:0000162	non_canonical_five_prime_splice_site	SO:0000835
4	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	1165590	SO:0000680	SO:0000851	non_canonical_start_codon	SO:0000316
4	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	1165591	SO:0000680	SO:0000851	non_canonical_start_codon	SO:0000836
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons." [SO:ke]	SO	1165592	SO:0000681	SO:0001411	aberrant_processed_transcript	SO:0000001
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	1165593	SO:0000683	SO:0001679	exonic_splice_enhancer	SO:0005836
4	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	SOFA	binding_site	biosapiens,SOFA	SOFA	sequence	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SO	1165594	SO:0000684	SO:0000410	nuclease_sensitive_site	SO:0000409
4	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	\N	nucleotide_to_protein_binding_site	SOFA	SOFA	sequence	"" []	SO	1165595	SO:0000685	SO:0000059	DNAseI_hypersensitive_site	SO:0001654
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	1165596	SO:0000686	SO:1000183	translocation_element	SO:0000240
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]	SO	1165597	SO:0000688	SO:0001410	golden_path	SO:0000001
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"A match against cDNA sequence." [SO:ke]	SO	1165598	SO:0000689	SO:0000343	cDNA_match	SO:0001410
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes a polycistronic transcript." [SO:xp]	SO	1165599	SO:0000690	SO:0000001	gene_with_polycistronic_transcript	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	1259869	SO:0000691	SO:0000104	cleaved_initiator_methionine	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	1805632	SO:0000691	SO:0001411	cleaved_initiator_methionine	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes a dicistronic transcript." [SO:xp]	SO	1165604	SO:0000692	SO:0001411	gene_with_dicistronic_transcript	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes an mRNA that is recoded." [SO:xp]	SO	1165605	SO:0000693	SO:0001411	gene_with_recoded_mRNA	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SO	1165606	SO:0000694	SO:0001059	SNP	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SO	1165607	SO:0000694	SO:0001411	SNP	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	SO	1165608	SO:0000696	SO:0000001	oligo	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	SO	1165609	SO:0000697	SO:0000704	gene_with_stop_codon_read_through	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	1259871	SO:0000698	SO:0000704	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of sequence where the validity of the base calling is questionable." [SO:ke]	SO	1165611	SO:0000701	SO:0001410	possible_base_call_error	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of sequence where there may have been an error in the assembly." [SO:ke]	SO	1165612	SO:0000702	SO:0001410	possible_assembly_error	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of sequence implicated in an experimental result." [SO:ke]	SO	1165613	SO:0000703	SO:0000001	experimental_result_region	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	SO	1165614	SO:0000705	SO:0000001	tandem_repeat	SO:0000110
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SOFA	primary_transcript	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	1165615	SO:0000706	SO:0000835	trans_splice_acceptor_site	SO:0000185
4	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	1165616	SO:0000706	SO:0000835	trans_splice_acceptor_site	SO:0000833
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	1165617	SO:0000707	SO:0000835	trans_splice_donor_site	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	1165618	SO:0000707	SO:0000835	trans_splice_donor_site	SO:0000833
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	1165619	SO:0000708	SO:0000162	SL1_acceptor_site	SO:0000835
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1165620	SO:0000709	SO:0000162	SL2_acceptor_site	SO:0000835
4	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	SO	1165621	SO:0000710	SO:0001217	gene_with_stop_codon_redefined_as_selenocysteine	SO:0000704
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene with mRNA recoded by translational bypass." [SO:xp]	SO	1259872	SO:0000711	SO:0001411	gene_with_mRNA_recoded_by_translational_bypass	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene encoding a transcript that has a translational frameshift." [SO:xp]	SO	1165623	SO:0000712	SO:0000704	gene_with_transcript_with_translational_frameshift	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A motif that is active in the DNA form of the sequence." [SO:ke]	SO	1165624	SO:0000713	SO:0001411	DNA_motif	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	SO	1165625	SO:0000714	SO:0000001	nucleotide_motif	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A motif that is active in RNA sequence." [SO:ke]	SO	1165626	SO:0000715	SO:0001411	RNA_motif	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	1679585	SO:0000716	SO:0000831	dicistronic_mRNA	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]	SO	1165629	SO:0000718	SO:0000001	blocked_reading_frame	SO:0000110
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	SOFA	experimental_feature	SOFA	SOFA	sequence	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SO	1165630	SO:0000719	SO:0001248	ultracontig	SO:0001410
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable element that is foreign." [SO:ke]	SO	1165631	SO:0000720	SO:0001037	foreign_transposable_element	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposable element that is foreign." [SO:ke]	SO	1165632	SO:0000720	SO:0001037	foreign_transposable_element	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes a dicistronic primary transcript." [SO:xp]	SO	1165633	SO:0000721	SO:0000704	gene_with_dicistronic_primary_transcript	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that encodes a polycistronic mRNA." [SO:xp]	SO	1165634	SO:0000722	SO:0000704	gene_with_dicistronic_mRNA	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]	SO	1165635	SO:0000723	SO:0000001	iDNA	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1259875	SO:0000724	SO:0000001	oriT	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens,SOFA	biological_region	SOFA	SOFA	sequence	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1165638	SO:0000725	SO:0000104	transit_peptide	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens,SOFA	region	SOFA	SOFA	sequence	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640457	SO:0000725	SO:0001411	transit_peptide	SO:0000001
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SO	1165640	SO:0000727	SO:0005836	CRM	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	1259876	SO:0000728	SO:0000104	intein	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	1805638	SO:0000728	SO:0001411	intein	SO:0000001
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]	SO	1165645	SO:0000729	SO:0000733	intein_containing	SO:0000400
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]	SO	1259878	SO:0000730	SO:0000001	gap	SO:0000110
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	1165648	SO:0000734	SO:0000673	exemplar_mRNA	SO:0000831
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]	SO	1165649	SO:0000742	SO:0000001	maxicircle	SO:0000110
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165650	SO:0000743	SO:0000735	apicoplast_sequence	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165651	SO:0000744	SO:0000735	chromoplast_sequence	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165652	SO:0000745	SO:0000735	chloroplast_sequence	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165653	SO:0000746	SO:0000735	cyanelle_sequence	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165654	SO:0000747	SO:0000735	leucoplast_sequence	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165655	SO:0000748	SO:0000735	proplastid_sequence	SO:0000400
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]	SO	1259879	SO:0000750	SO:0000001	amplification_origin	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"" []	SO	1165658	SO:0000752	SO:0000831	gene_group_regulatory_region	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]	SO	1259880	SO:0000753	SO:0000001	clone_insert	SO:0000110
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	1165660	SO:0000754	SO:0000695	lambda_vector	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	1165661	SO:0000754	SO:0001411	lambda_vector	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"" []	SO	1165662	SO:0000755	SO:0000695	plasmid_vector	SO:0001409
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2081461	SO:0000755	SO:0000001	plasmid_vector	SO:0000110
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]	SO	1165664	SO:0000756	SO:0000443	cDNA	SO:0000400
4	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"" []	SO	1165665	SO:0000757	SO:0000348	single_stranded_cDNA	SO:0000443
4	"An attribute to describe the kind of biological sequence." [SO:ke]	\N	polymer_attribute	\N	\N	sequence	"" []	SO	1165666	SO:0000758	SO:0000348	double_stranded_cDNA	SO:0000443
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	1165667	SO:0000766	SO:0000233	pyrrolysyl_tRNA	SO:0000673
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid that may integrate with a chromosome." [SO:ma]	SO	1165668	SO:0000768	SO:0001411	episome	SO:0000001
4	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	1165669	SO:0000769	SO:0000370	tmRNA_coding_piece	SO:0000655
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	1165670	SO:0000769	SO:0000833	tmRNA_coding_piece	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	1165671	SO:0000769	SO:0000833	tmRNA_coding_piece	SO:0001411
4	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	\N	ncRNA	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	1165672	SO:0000770	SO:0000370	tmRNA_acceptor_piece	SO:0000655
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	1165673	SO:0000770	SO:0000833	tmRNA_acceptor_piece	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	1165674	SO:0000770	SO:0000833	tmRNA_acceptor_piece	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	SO	1640476	SO:0000772	SO:0000001	genomic_island	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]	SO	1165676	SO:0000772	SO:0001411	genomic_island	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	SO	1165677	SO:0000773	SO:0001037	pathogenic_island	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	SO	1165678	SO:0000773	SO:0001037	pathogenic_island	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	1165679	SO:0000774	SO:0001037	metabolic_island	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	1165680	SO:0000774	SO:0001037	metabolic_island	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	SO	1165681	SO:0000775	SO:0001037	adaptive_island	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	SO	1165682	SO:0000775	SO:0001037	adaptive_island	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	1165683	SO:0000776	SO:0001037	symbiosis_island	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	1165684	SO:0000776	SO:0001037	symbiosis_island	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A non functional descendant of an rRNA." [SO:ke]	SO	1165685	SO:0000777	SO:0000001	pseudogenic_rRNA	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A non functional descendent of a tRNA." [SO:ke]	SO	1165686	SO:0000778	SO:0000001	pseudogenic_tRNA	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An episome that is engineered." [SO:xp]	SO	1165687	SO:0000779	SO:0001235	engineered_episome	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An episome that is engineered." [SO:xp]	SO	2081473	SO:0000779	SO:0000001	engineered_episome	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An episome that is engineered." [SO:xp]	SO	1165689	SO:0000779	SO:0001409	engineered_episome	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1679586	SO:0000785	SO:0000001	cloned_region	SO:0000110
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A mini_gene that rescues." [SO:xp]	SO	1165694	SO:0000795	SO:0000717	rescue_mini_gene	SO:0001410
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	SO	1165695	SO:0000796	SO:0001037	transgenic_transposable_element	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	SO	1165696	SO:0000796	SO:0001037	transgenic_transposable_element	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	1805640	SO:0000797	SO:0000001	natural_transposable_element	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"TE that exists (or existed) in nature." [FB:mc]	SO	1259885	SO:0000797	SO:0001411	natural_transposable_element	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	1165701	SO:0000798	SO:0001037	engineered_transposable_element	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	1165702	SO:0000798	SO:0001037	engineered_transposable_element	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	1165705	SO:0000799	SO:0001409	engineered_foreign_transposable_element	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	1259886	SO:0000799	SO:0001037	engineered_foreign_transposable_element	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	1259887	SO:0000799	SO:0001037	engineered_foreign_transposable_element	SO:0001411
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	1165708	SO:0000800	SO:0001507	assortment_derived_duplication	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	1165709	SO:0000800	SO:0001524	assortment_derived_duplication	SO:0001506
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	1165710	SO:0000801	SO:0001507	assortment_derived_deficiency_plus_duplication	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	1165711	SO:0000801	SO:0001524	assortment_derived_deficiency_plus_duplication	SO:0001506
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	1165712	SO:0000802	SO:0001507	assortment_derived_deficiency	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	1165713	SO:0000802	SO:0001524	assortment_derived_deficiency	SO:0001506
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	1165714	SO:0000803	SO:0001507	assortment_derived_aneuploid	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	1165715	SO:0000803	SO:0001524	assortment_derived_aneuploid	SO:0001506
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A tag that is engineered." [SO:xp]	SO	1165717	SO:0000807	SO:0000695	engineered_tag	SO:0001409
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A cDNA clone that has been validated." [SO:xp]	SO	1165719	SO:0000808	SO:0000695	validated_cDNA_clone	SO:0001409
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A cDNA clone that is invalid." [SO:xp]	SO	1165720	SO:0000809	SO:0000695	invalidated_cDNA_clone	SO:0001409
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A cDNA clone invalidated because it is chimeric." [SO:xp]	SO	1165721	SO:0000810	SO:0000151	chimeric_cDNA_clone	SO:0000695
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A cDNA clone invalidated by genomic contamination." [SO:xp]	SO	1165722	SO:0000811	SO:0000151	genomically_contaminated_cDNA_clone	SO:0000695
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A cDNA clone invalidated by polyA priming." [SO:xp]	SO	1165723	SO:0000812	SO:0000151	polyA_primed_cDNA_clone	SO:0000695
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A cDNA invalidated clone by partial processing." [SO:xp]	SO	1165724	SO:0000813	SO:0000151	partially_processed_cDNA_clone	SO:0000695
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]	SO	1165725	SO:0000815	SO:0001410	mini_gene	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that rescues." [SO:xp]	SO	1165726	SO:0000816	SO:0000001	rescue_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that rescues." [SO:xp]	SO	1259888	SO:0000818	SO:0000001	wild_type_rescue_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in a mitochondria." [SO:xp]	SO	1165728	SO:0000819	SO:0001411	mitochondrial_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in a chloroplast." [SO:xp]	SO	1165729	SO:0000820	SO:0001411	chloroplast_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in a chromoplast." [SO:xp]	SO	1165730	SO:0000821	SO:0001411	chromoplast_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in a cyanelle." [SO:xp]	SO	1165731	SO:0000822	SO:0001411	cyanelle_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome with origin in a leucoplast." [SO:xp]	SO	1165732	SO:0000823	SO:0001411	leucoplast_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in a macronucleus." [SO:xp]	SO	1165733	SO:0000824	SO:0001411	macronuclear_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in a micronucleus." [SO:xp]	SO	1165734	SO:0000825	SO:0001411	micronuclear_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in a nucleus." [SO:xp]	SO	1165735	SO:0000828	SO:0001411	nuclear_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in a nucleomorph." [SO:xp]	SO	1165736	SO:0000829	SO:0001411	nucleomorphic_chromosome	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a mature transcript." [SO:ke]	SO	1165739	SO:0000834	SO:0000831	mature_transcript_region	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of a mature transcript." [SO:ke]	SO	1679588	SO:0000834	SO:0000001	mature_transcript_region	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	1165741	SO:0000835	SO:0000831	primary_transcript_region	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A part of a primary transcript." [SO:ke]	SO	1679589	SO:0000835	SO:0000001	primary_transcript_region	SO:0000110
4	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	1165743	SO:0000836	SO:0000673	mRNA_region	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	2081487	SO:0000836	SO:0001411	mRNA_region	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	1165745	SO:0000837	SO:0000233	UTR_region	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	1165746	SO:0000837	SO:0000833	UTR_region	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	1165747	SO:0000837	SO:0000833	UTR_region	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	1259889	SO:0000838	SO:0000673	rRNA_primary_transcript_region	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	2279407	SO:0000838	SO:0001411	rRNA_primary_transcript_region	SO:0000001
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	1679590	SO:0000841	SO:0000673	spliceosomal_intron_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	2548806	SO:0000841	SO:0001411	spliceosomal_intron_region	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	2081492	SO:0000847	SO:0000673	tmRNA_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	2548807	SO:0000847	SO:0001411	tmRNA_region	SO:0000001
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	1165757	SO:0000847	SO:0000655	tmRNA_region	SO:0000233
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2731407	SO:0000848	SO:0000001	LTR_component	SO:0000110
4	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1165759	SO:0000848	SO:0000180	LTR_component	SO:0000101
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706713	SO:0000848	SO:0001411	LTR_component	SO:0000001
4	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1165761	SO:0000849	SO:0000186	three_prime_LTR_component	SO:0000180
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165762	SO:0000849	SO:0000657	three_prime_LTR_component	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165763	SO:0000849	SO:0001412	three_prime_LTR_component	SO:0000001
4	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1165764	SO:0000850	SO:0000186	five_prime_LTR_component	SO:0000180
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165765	SO:0000850	SO:0000657	five_prime_LTR_component	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165766	SO:0000850	SO:0001412	five_prime_LTR_component	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	1259890	SO:0000851	SO:0000233	CDS_region	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	1259891	SO:0000851	SO:0000833	CDS_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	1259892	SO:0000851	SO:0000833	CDS_region	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	1259893	SO:0000852	SO:0000831	exon_region	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of an exon." [RSC:cb]	SO	2102386	SO:0000852	SO:0000001	exon_region	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region that is homologous to another region." [SO:ke]	SO	1165772	SO:0000853	SO:0000001	homologous_region	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A homologous_region that is paralogous to another region." [SO:ke]	SO	1165773	SO:0000854	SO:0001410	paralogous_region	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A homologous_region that is orthologous to another region." [SO:ke]	SO	1165774	SO:0000855	SO:0001410	orthologous_region	SO:0000001
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]	SO	1165775	SO:0000858	SO:0000733	orthologous	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]	SO	1165776	SO:0000859	SO:0000733	paralogous	SO:0000400
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript that is capped." [SO:xp]	SO	1165777	SO:0000861	SO:0000831	capped_primary_transcript	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA that is capped." [SO:xp]	SO	1165778	SO:0000862	SO:0000673	capped_mRNA	SO:0000831
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]	SO	1165779	SO:0000864	SO:0000733	exemplar	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]	SO	1165780	SO:0000865	SO:0000733	frameshift	SO:0000400
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A frameshift caused by deleting one base." [SO:ke]	SO	1165781	SO:0000866	SO:0000237	minus_1_frameshift	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A frameshift caused by deleting two bases." [SO:ke]	SO	1165782	SO:0000867	SO:0000237	minus_2_frameshift	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A frameshift caused by inserting one base." [SO:ke]	SO	1165783	SO:0000868	SO:0000237	plus_1_frameshift	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A frameshift caused by inserting two bases." [SO:ke]	SO	1165784	SO:0000869	SO:0000237	plus_2_framshift	SO:0000733
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA that is polyadenylated." [SO:xp]	SO	1165785	SO:0000871	SO:0000673	polyadenylated_mRNA	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	1259895	SO:0000872	SO:0000831	trans_spliced_mRNA	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is edited." [SO:ke]	SO	1165788	SO:0000873	SO:0001411	edited_transcript	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that has been edited by A to I substitution." [SO:ke]	SO	1165789	SO:0000874	SO:0000831	edited_transcript_by_A_to_I_substitution	SO:0001411
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that contains the code for two gene products." [SO:ke]	SO	1165790	SO:0000879	SO:0000733	dicistronic	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]	SO	1165791	SO:0000881	SO:0000733	recoded	SO:0000400
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing the alteration of codon meaning." [SO:ke]	SO	1165792	SO:0000882	SO:0000237	codon_redefined	SO:0000733
4	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	1165793	SO:0000883	SO:0000851	stop_codon_read_through	SO:0000316
4	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	1165794	SO:0000883	SO:0000851	stop_codon_read_through	SO:0000836
4	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	1165795	SO:0000884	SO:0000360	stop_codon_redefined_as_pyrrolysine	SO:0000851
4	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	1165796	SO:0000885	SO:0000360	stop_codon_redefined_as_selenocysteine	SO:0000851
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Recoded mRNA where a block of nucleotides is not translated." [SO:ke]	SO	1165797	SO:0000886	SO:0000237	recoded_by_translational_bypass	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"Recoding by frameshifting a particular site." [SO:ke]	SO	1165798	SO:0000887	SO:0000237	translationally_frameshifted	SO:0000733
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is maternally_imprinted." [SO:xp]	SO	1259896	SO:0000888	SO:0000001	maternally_imprinted_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is paternally imprinted." [SO:xp]	SO	1259897	SO:0000889	SO:0000001	paternally_imprinted_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is post translationally regulated." [SO:xp]	SO	1165801	SO:0000890	SO:0000001	post_translationally_regulated_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is negatively autoreguated." [SO:xp]	SO	1165802	SO:0000891	SO:0000001	negatively_autoregulated_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is positively autoregulated." [SO:xp]	SO	1165803	SO:0000892	SO:0000001	positively_autoregulated_gene	SO:0000110
4	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	SO	1165804	SO:0000893	SO:0000119	silenced	SO:0000401
4	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	SO	1165805	SO:0000894	SO:0000123	silenced_by_DNA_modification	SO:0000119
4	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	1165806	SO:0000895	SO:0000126	silenced_by_DNA_methylation	SO:0000123
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is translationally regulated." [SO:xp]	SO	1165807	SO:0000896	SO:0000001	translationally_regulated_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is allelically_excluded." [SO:xp]	SO	1165808	SO:0000897	SO:0001411	allelically_excluded_gene	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is epigenetically modified." [SO:ke]	SO	1165809	SO:0000898	SO:0000001	epigenetically_modified_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]	SO	1165810	SO:0000902	SO:0000001	transgene	SO:0000110
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]	SO	1165811	SO:0000904	SO:0000733	rearranged_at_DNA_level	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]	SO	1165812	SO:0000907	SO:0000733	supported_by_sequence_similarity	SO:0000400
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]	SO	1165813	SO:0000908	SO:0000905	supported_by_domain_match	SO:0000733
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]	SO	1165814	SO:0000909	SO:0000905	supported_by_EST_or_cDNA	SO:0000733
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165815	SO:0000910	SO:0000733	orphan	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]	SO	1165816	SO:0000911	SO:0000733	predicted_by_ab_initio_computation	SO:0000400
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1165817	SO:0000912	SO:0001070	asx_turn	SO:0000839
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A clone insert made from cDNA." [SO:xp]	SO	1259898	SO:0000913	SO:0001409	cloned_cDNA_insert	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A clone insert made from genomic DNA." [SO:xp]	SO	1259899	SO:0000914	SO:0001409	cloned_genomic_insert	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA that is edited." [SO:xp]	SO	1259902	SO:0000929	SO:0000831	edited_mRNA	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	1640574	SO:0000930	SO:0000673	guide_RNA_region	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	2279414	SO:0000930	SO:0001411	guide_RNA_region	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	1165829	SO:0000930	SO:0000233	guide_RNA_region	SO:0000673
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	1165830	SO:0000931	SO:0000655	anchor_region	SO:0000233
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	1165831	SO:0000931	SO:0000833	anchor_region	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	1165832	SO:0000931	SO:0000833	anchor_region	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1165833	SO:0000932	SO:0000673	pre_edited_mRNA	SO:0000831
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]	SO	1165834	SO:0000934	SO:0001411	miRNA_target_site	SO:0000001
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	1165835	SO:0000935	SO:0000234	edited_CDS	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	1165836	SO:0000935	SO:0000834	edited_CDS	SO:0000833
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1165837	SO:0000936	SO:0000299	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000669
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1165838	SO:0000938	SO:0000299	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000669
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1165839	SO:0000939	SO:0000299	vertebrate_immune_system_gene_recombination_signal_feature	SO:0000669
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]	SO	1165840	SO:0000941	SO:0001411	recombinationally_rearranged_vertebrate_immune_system_gene	SO:0000001
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	1165841	SO:0000942	SO:0000299	attP_site	SO:0000669
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	1165842	SO:0000942	SO:0001038	attP_site	SO:0001037
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	1165843	SO:0000942	SO:0001235	attP_site	SO:0001411
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	1165844	SO:0000943	SO:0000299	attB_site	SO:0000669
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	1165845	SO:0000944	SO:0000299	attL_site	SO:0000669
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	1165846	SO:0000945	SO:0000299	attR_site	SO:0000669
4	"" []	\N	recombination_feature	\N	\N	sequence	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	SO	1165847	SO:0000946	SO:0000669	integration_excision_site	SO:0000298
4	"" []	\N	recombination_feature	\N	\N	sequence	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	SO	1165848	SO:0000947	SO:0000669	resolution_site	SO:0000298
4	"" []	\N	recombination_feature	\N	\N	sequence	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	SO	1165849	SO:0000948	SO:0000669	inversion_site	SO:0000298
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	1165850	SO:0000949	SO:0000299	dif_site	SO:0000669
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	1165851	SO:0000950	SO:0000299	attC_site	SO:0000669
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	1165852	SO:0000950	SO:0001037	attC_site	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	1165853	SO:0000950	SO:0001037	attC_site	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640602	SO:0000951	SO:0000831	eukaryotic_terminator	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1165855	SO:0000951	SO:0005836	eukaryotic_terminator	SO:0000831
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An origin of vegetative replication in plasmids and phages." [SO:as]	SO	1259903	SO:0000952	SO:0000001	oriV	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An origin of bacterial chromosome replication." [SO:as]	SO	1259904	SO:0000953	SO:0000001	oriC	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	SO	1165860	SO:0000954	SO:0001411	DNA_chromosome	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	SO	1165861	SO:0000955	SO:0001235	double_stranded_DNA_chromosome	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	SO	1165862	SO:0000956	SO:0001235	single_stranded_DNA_chromosome	SO:0001411
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	SO	1165863	SO:0000957	SO:0000340	linear_double_stranded_DNA_chromosome	SO:0001235
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	SO	1165864	SO:0000958	SO:0000340	circular_double_stranded_DNA_chromosome	SO:0001235
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	SO	1165865	SO:0000959	SO:0000340	linear_single_stranded_DNA_chromosome	SO:0001235
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	1165866	SO:0000960	SO:0000340	circular_single_stranded_DNA_chromosome	SO:0001235
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	SO	1165867	SO:0000961	SO:0001411	RNA_chromosome	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	SO	1165868	SO:0000962	SO:0001235	single_stranded_RNA_chromosome	SO:0001411
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	SO	1165869	SO:0000963	SO:0000340	linear_single_stranded_RNA_chromosome	SO:0001235
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	SO	1165870	SO:0000964	SO:0000340	linear_double_stranded_RNA_chromosome	SO:0001235
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	SO	1165871	SO:0000965	SO:0001235	double_stranded_RNA_chromosome	SO:0001411
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	1165872	SO:0000966	SO:0000340	circular_single_stranded_RNA_chromosome	SO:0001235
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	SO	1165873	SO:0000967	SO:0000340	circular_double_stranded_RNA_chromosome	SO:0001235
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	1165874	SO:0000973	SO:0000101	insertion_sequence	SO:0001039
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165875	SO:0000975	SO:0000704	minicircle_gene	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640618	SO:0000975	SO:0001411	minicircle_gene	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1165877	SO:0000977	SO:0000831	anchor_binding_site	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1679594	SO:0000977	SO:0000001	anchor_binding_site	SO:0000110
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	1165879	SO:0000978	SO:0000655	template_region	SO:0000233
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	1165880	SO:0000978	SO:0000833	template_region	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	1165881	SO:0000978	SO:0000833	template_region	SO:0001411
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A non-protein_coding gene that encodes a guide_RNA." [SO:ma]	SO	1165882	SO:0000979	SO:0000733	gRNA_encoding	SO:0000400
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]	SO	1165883	SO:0000980	SO:0000001	minicircle	SO:0000110
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1165884	SO:0000981	SO:0000673	rho_dependent_bacterial_terminator	SO:0000831
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	1165885	SO:0000981	SO:0001679	rho_dependent_bacterial_terminator	SO:0005836
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1165886	SO:0000982	SO:0000673	rho_independent_bacterial_terminator	SO:0000831
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	1165887	SO:0000982	SO:0001679	rho_independent_bacterial_terminator	SO:0005836
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	1165888	SO:0000989	SO:0000673	class_II_RNA	SO:0000831
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	1165889	SO:0000990	SO:0000673	class_I_RNA	SO:0000831
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165890	SO:0000991	SO:0000443	genomic_DNA	SO:0000400
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"" []	SO	1165891	SO:0000992	SO:0000151	BAC_cloned_genomic_insert	SO:0000695
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"" []	SO	1640630	SO:0000992	SO:0000695	BAC_cloned_genomic_insert	SO:0001409
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1165893	SO:0000995	SO:0000673	consensus_mRNA	SO:0000831
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1165895	SO:0000996	SO:0000001	predicted_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259905	SO:0000997	SO:0000001	gene_fragment	SO:0000110
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	1165898	SO:0000998	SO:0000835	recursive_splice_site	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	1165899	SO:0000998	SO:0000835	recursive_splice_site	SO:0000833
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	2764359	SO:0000999	SO:0001410	BAC_end	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	1165902	SO:0000999	SO:0000148	BAC_end	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	1165903	SO:0000999	SO:0000148	BAC_end	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	2279422	SO:0000999	SO:0000353	BAC_end	SO:0001248
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	1165905	SO:0000999	SO:0000151	BAC_end	SO:0000695
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	1165906	SO:0000999	SO:0001235	BAC_end	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	1165907	SO:0001000	SO:0000655	rRNA_16S	SO:0000233
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	1165908	SO:0001001	SO:0000655	rRNA_23S	SO:0000233
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	1165909	SO:0001002	SO:0000655	rRNA_25S	SO:0000233
4	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	1165910	SO:0001003	SO:0000180	solo_LTR	SO:0000101
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	2706741	SO:0001003	SO:0001411	solo_LTR	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	SO	1165912	SO:0001006	SO:0001037	prophage	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	SO	1165913	SO:0001006	SO:0001037	prophage	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	SO	1165914	SO:0001007	SO:0001037	cryptic_prophage	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	SO	1165915	SO:0001007	SO:0001037	cryptic_prophage	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]	SO	1165916	SO:0001008	SO:0000002	tetraloop	SO:0001411
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	SO	1165917	SO:0001009	SO:0000695	DNA_constraint_sequence	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]	SO	1165918	SO:0001010	SO:0001411	i_motif	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]	SO	1165919	SO:0001011	SO:0000695	PNA_oligo	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequence with catalytic activity." [SO:cb]	SO	1165920	SO:0001012	SO:0001409	DNAzyme	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	SO	1165921	SO:0001013	SO:0001059	MNP	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	SO	1165922	SO:0001013	SO:0001411	MNP	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1259907	SO:0001014	SO:0000673	intron_domain	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2279423	SO:0001014	SO:0001411	intron_domain	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]	SO	1165925	SO:0001015	SO:0001411	wobble_base_pair	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	1679595	SO:0001016	SO:0000185	internal_guide_sequence	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	1679596	SO:0001016	SO:0000833	internal_guide_sequence	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	1679597	SO:0001016	SO:0000833	internal_guide_sequence	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]	SO	1165932	SO:0001018	SO:0000001	epitope	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1165933	SO:0001021	SO:0001411	chromosome_breakpoint	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	1165934	SO:0001022	SO:0001235	inversion_breakpoint	SO:0001411
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1165935	SO:0001032	SO:0000735	mitochondrial_DNA	SO:0000400
4	"" []	\N	sequence_location	\N	\N	sequence	"" []	SO	1165936	SO:0001033	SO:0000736	chloroplast_DNA	SO:0000735
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	1259914	SO:0001034	SO:0000185	mirtron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	1259915	SO:0001034	SO:0000833	mirtron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	1259916	SO:0001034	SO:0000833	mirtron	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	SO	1165942	SO:0001035	SO:0000673	piRNA	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	1165943	SO:0001036	SO:0000233	arginyl_tRNA	SO:0000673
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A plasmid sequence that is integrated within the host chromosome." [SO:ke]	SO	1640669	SO:0001040	SO:0000001	integrated_plasmid	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid sequence that is integrated within the host chromosome." [SO:ke]	SO	1165947	SO:0001040	SO:0001411	integrated_plasmid	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]	SO	1259917	SO:0001041	SO:0000001	viral_sequence	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	1165950	SO:0001042	SO:0001037	phage_sequence	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	1165951	SO:0001042	SO:0001037	phage_sequence	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	1640671	SO:0001042	SO:0001411	phage_sequence	SO:0000001
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	1165953	SO:0001043	SO:0000299	attCtn_site	SO:0000669
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	1165954	SO:0001043	SO:0000101	attCtn_site	SO:0001039
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]	SO	1165955	SO:0001044	SO:0001411	nuclear_mt_pseudogene	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]	SO	1640675	SO:0001045	SO:0000001	cointegrated_plasmid	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]	SO	1165957	SO:0001045	SO:0001411	cointegrated_plasmid	SO:0000001
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	1165958	SO:0001046	SO:0000299	IRLinv_site	SO:0000669
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	1165959	SO:0001047	SO:0000299	IRRinv_site	SO:0000669
4	"" []	\N	recombination_feature	\N	\N	sequence	"A region located within an inversion site." [SO:ke]	SO	1165960	SO:0001048	SO:0000669	inversion_site_part	SO:0000298
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	SO	1165961	SO:0001049	SO:0001037	defective_conjugative_transposon	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	SO	1165962	SO:0001049	SO:0001037	defective_conjugative_transposon	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	1640681	SO:0001050	SO:0000001	repeat_fragment	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A portion of a repeat, interrupted by the insertion of another element." [SO:ke]	SO	1165964	SO:0001050	SO:0001411	repeat_fragment	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	2441477	SO:0001054	SO:0000001	transposon_fragment	SO:0000110
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	1165966	SO:0001054	SO:0001039	transposon_fragment	SO:0001037
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SO	1165967	SO:0001055	SO:0000831	transcriptional_cis_regulatory_region	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A regulatory_region that modulates splicing." [SO:ke]	SO	1165968	SO:0001056	SO:0000831	splicing_regulatory_region	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	SO	1165969	SO:0001058	SO:0005836	promoter_targeting_sequence	SO:0000831
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	1679598	SO:0001061	SO:0000104	propeptide_cleavage_site	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	2165149	SO:0001061	SO:0001411	propeptide_cleavage_site	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	1259922	SO:0001062	SO:0000104	propeptide	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	1805664	SO:0001062	SO:0001411	propeptide	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens,SOFA	sequence_feature	SOFA	SOFA	sequence	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	SO	1259924	SO:0001063	SO:0000001	immature_peptide_region	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	1259925	SO:0001064	SO:0000104	active_peptide	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	1805666	SO:0001064	SO:0001411	active_peptide	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]	SO	1259927	SO:0001066	SO:0000001	compositionally_biased_region_of_peptide	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	SO	1165984	SO:0001067	SO:0000104	polypeptide_motif	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	SO	1640690	SO:0001067	SO:0001411	polypeptide_motif	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	SO	1165986	SO:0001068	SO:0000104	polypeptide_repeat	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	SO	1640692	SO:0001068	SO:0001411	polypeptide_repeat	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	SO	1259928	SO:0001070	SO:0000001	polypeptide_structural_region	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	SO	1165990	SO:0001071	SO:0000104	membrane_structure	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	SO	1640694	SO:0001071	SO:0001411	membrane_structure	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	1259929	SO:0001072	SO:0000104	extramembrane_polypeptide_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	1805671	SO:0001072	SO:0001411	extramembrane_polypeptide_region	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	1259931	SO:0001073	SO:0000839	cytoplasmic_polypeptide_region	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	1259932	SO:0001073	SO:0000839	cytoplasmic_polypeptide_region	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	1259933	SO:0001074	SO:0000839	non_cytoplasmic_polypeptide_region	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	1259934	SO:0001074	SO:0000839	non_cytoplasmic_polypeptide_region	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	1259935	SO:0001075	SO:0000104	intramembrane_polypeptide_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	1805677	SO:0001075	SO:0001411	intramembrane_polypeptide_region	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	1259937	SO:0001076	SO:0000839	membrane_peptide_loop	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	1259938	SO:0001076	SO:0000839	membrane_peptide_loop	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	1259939	SO:0001077	SO:0000839	transmembrane_polypeptide_region	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	1259940	SO:0001077	SO:0000839	transmembrane_polypeptide_region	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	SO	1166008	SO:0001078	SO:0000104	polypeptide_secondary_structure	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	SO	1640706	SO:0001078	SO:0001411	polypeptide_secondary_structure	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	SO	1166010	SO:0001079	SO:0000104	polypeptide_structural_motif	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	SO	1640708	SO:0001079	SO:0001411	polypeptide_structural_motif	SO:0000001
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	1166012	SO:0001080	SO:0000839	coiled_coil	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	1166013	SO:0001080	SO:0000839	coiled_coil	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	1166014	SO:0001081	SO:0000839	helix_turn_helix	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	1166015	SO:0001081	SO:0000839	helix_turn_helix	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]	SO	1166016	SO:0001082	SO:0000001	polypeptide_sequencing_information	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]	SO	1166017	SO:0001083	SO:0001410	non_adjacent_residues	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]	SO	1166018	SO:0001084	SO:0001410	non_terminal_residue	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]	SO	1166019	SO:0001085	SO:0001410	sequence_conflict	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]	SO	1166020	SO:0001086	SO:0001410	sequence_uncertainty	SO:0000001
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	1166021	SO:0001089	SO:0100021	post_translationally_modified_region	SO:0000839
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	2706746	SO:0001092	SO:0001411	polypeptide_metal_contact	SO:0000001
4	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	1166023	SO:0001092	SO:0001067	polypeptide_metal_contact	SO:0100021
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	2706747	SO:0001093	SO:0001411	protein_protein_contact	SO:0000001
4	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	1166025	SO:0001093	SO:0001067	protein_protein_contact	SO:0100021
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	1166026	SO:0001094	SO:0000409	polypeptide_calcium_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	1166027	SO:0001094	SO:0100001	polypeptide_calcium_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	1166028	SO:0001095	SO:0000409	polypeptide_cobalt_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	1166029	SO:0001095	SO:0100001	polypeptide_cobalt_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	1166030	SO:0001096	SO:0000409	polypeptide_copper_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	1166031	SO:0001096	SO:0100001	polypeptide_copper_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	1166032	SO:0001097	SO:0000409	polypeptide_iron_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	1166033	SO:0001097	SO:0100001	polypeptide_iron_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	1166034	SO:0001098	SO:0000409	polypeptide_magnesium_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	1166035	SO:0001098	SO:0100001	polypeptide_magnesium_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	1166036	SO:0001099	SO:0000409	polypeptide_manganese_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	1166037	SO:0001099	SO:0100001	polypeptide_manganese_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	1166038	SO:0001100	SO:0000409	polypeptide_molybdenum_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	1166039	SO:0001100	SO:0100001	polypeptide_molybdenum_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	1166040	SO:0001101	SO:0000409	polypeptide_nickel_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	1166041	SO:0001101	SO:0100001	polypeptide_nickel_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	1166042	SO:0001102	SO:0000409	polypeptide_tungsten_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	1166043	SO:0001102	SO:0100001	polypeptide_tungsten_ion_contact_site	SO:0001067
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	1166044	SO:0001103	SO:0000409	polypeptide_zinc_ion_contact_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	biosapiens	polypeptide_motif	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	1166045	SO:0001103	SO:0100001	polypeptide_zinc_ion_contact_site	SO:0001067
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	2712711	SO:0001104	SO:0000001	catalytic_residue	SO:0000110
4	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	1166048	SO:0001104	SO:0001067	catalytic_residue	SO:0100021
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	2706768	SO:0001105	SO:0001411	polypeptide_ligand_contact	SO:0000001
4	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	1166050	SO:0001105	SO:0001067	polypeptide_ligand_contact	SO:0100021
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166051	SO:0001106	SO:0000839	asx_motif	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166052	SO:0001106	SO:0000839	asx_motif	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166053	SO:0001107	SO:0000839	beta_bulge	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166054	SO:0001107	SO:0000839	beta_bulge	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166055	SO:0001108	SO:0000839	beta_bulge_loop	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166056	SO:0001108	SO:0000839	beta_bulge_loop	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166057	SO:0001109	SO:0001070	beta_bulge_loop_five	SO:0000839
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166058	SO:0001110	SO:0001070	beta_bulge_loop_six	SO:0000839
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	1166059	SO:0001111	SO:0000839	beta_strand	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	1166060	SO:0001111	SO:0000839	beta_strand	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	1166061	SO:0001112	SO:0001070	antiparallel_beta_strand	SO:0000839
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	1166062	SO:0001113	SO:0001070	parallel_beta_strand	SO:0000839
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	1166063	SO:0001114	SO:0000839	peptide_helix	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	1166064	SO:0001114	SO:0000839	peptide_helix	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	1166065	SO:0001115	SO:0001070	left_handed_peptide_helix	SO:0000839
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	1166066	SO:0001116	SO:0001070	right_handed_peptide_helix	SO:0000839
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	1166067	SO:0001117	SO:0001078	alpha_helix	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	1166068	SO:0001118	SO:0001078	pi_helix	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	1166069	SO:0001119	SO:0001078	three_ten_helix	SO:0001070
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166070	SO:0001120	SO:0000839	polypeptide_nest_motif	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166071	SO:0001120	SO:0000839	polypeptide_nest_motif	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166072	SO:0001121	SO:0001070	polypeptide_nest_left_right_motif	SO:0000839
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166073	SO:0001122	SO:0001070	polypeptide_nest_right_left_motif	SO:0000839
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166074	SO:0001123	SO:0000839	schellmann_loop	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166075	SO:0001123	SO:0000839	schellmann_loop	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166076	SO:0001124	SO:0001070	schellmann_loop_seven	SO:0000839
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166077	SO:0001125	SO:0001070	schellmann_loop_six	SO:0000839
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166078	SO:0001126	SO:0000839	serine_threonine_motif	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166079	SO:0001126	SO:0000839	serine_threonine_motif	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166080	SO:0001127	SO:0000839	serine_threonine_staple_motif	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166081	SO:0001127	SO:0000839	serine_threonine_staple_motif	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	1166082	SO:0001128	SO:0000839	polypeptide_turn_motif	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	1166083	SO:0001128	SO:0000839	polypeptide_turn_motif	SO:0001411
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166084	SO:0001129	SO:0001078	asx_turn_left_handed_type_one	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166085	SO:0001130	SO:0001078	asx_turn_left_handed_type_two	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166086	SO:0001131	SO:0001078	asx_turn_right_handed_type_two	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166087	SO:0001132	SO:0001078	asx_turn_right_handed_type_one	SO:0001070
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166088	SO:0001133	SO:0001070	beta_turn	SO:0000839
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166089	SO:0001134	SO:0001078	beta_turn_left_handed_type_one	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166090	SO:0001135	SO:0001078	beta_turn_left_handed_type_two	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166091	SO:0001136	SO:0001078	beta_turn_right_handed_type_one	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166092	SO:0001137	SO:0001078	beta_turn_right_handed_type_two	SO:0001070
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166093	SO:0001138	SO:0001070	gamma_turn	SO:0000839
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166094	SO:0001139	SO:0001078	gamma_turn_classic	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166095	SO:0001140	SO:0001078	gamma_turn_inverse	SO:0001070
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166096	SO:0001141	SO:0001070	serine_threonine_turn	SO:0000839
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166097	SO:0001142	SO:0001078	st_turn_left_handed_type_one	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166098	SO:0001143	SO:0001078	st_turn_left_handed_type_two	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166099	SO:0001144	SO:0001078	st_turn_right_handed_type_one	SO:0001070
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1166100	SO:0001145	SO:0001078	st_turn_right_handed_type_two	SO:0001070
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]	SO	1259942	SO:0001146	SO:0000001	polypeptide_variation_site	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	SO	1166103	SO:0001147	SO:0000104	natural_variant_site	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	SO	1640810	SO:0001147	SO:0001411	natural_variant_site	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	SO	1166105	SO:0001148	SO:0000104	mutated_variant_site	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	SO	1640812	SO:0001148	SO:0001411	mutated_variant_site	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	SO	1166107	SO:0001149	SO:0000104	alternate_sequence_site	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	SO	1640814	SO:0001149	SO:0001411	alternate_sequence_site	SO:0000001
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	1166109	SO:0001150	SO:0001078	beta_turn_type_six	SO:0001070
4	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	1166110	SO:0001151	SO:0001128	beta_turn_type_six_a	SO:0001078
4	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"" []	SO	1166111	SO:0001152	SO:0001133	beta_turn_type_six_a_one	SO:0001128
4	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	biosapiens	polypeptide_turn_motif	biosapiens	biosapiens	sequence	"" []	SO	1166112	SO:0001153	SO:0001133	beta_turn_type_six_a_two	SO:0001128
4	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	1166113	SO:0001154	SO:0001128	beta_turn_type_six_b	SO:0001078
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	1166114	SO:0001155	SO:0001078	beta_turn_type_eight	SO:0001070
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	1166115	SO:0001156	SO:0001683	DRE_motif	SO:0001411
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	1166116	SO:0001156	SO:0000167	DRE_motif	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	SO	1166117	SO:0001157	SO:0000714	DMv4_motif	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	1166118	SO:0001158	SO:0001683	E_box_motif	SO:0001411
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	1166119	SO:0001158	SO:0000167	E_box_motif	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	1166120	SO:0001159	SO:0000714	DMv5_motif	SO:0001683
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	1166121	SO:0001159	SO:0000167	DMv5_motif	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	1166122	SO:0001160	SO:0000714	DMv3_motif	SO:0001683
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	1166123	SO:0001160	SO:0000167	DMv3_motif	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	1166124	SO:0001161	SO:0000714	DMv2_motif	SO:0001683
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	1166125	SO:0001161	SO:0000167	DMv2_motif	SO:0001055
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	1166126	SO:0001162	SO:0000713	MTE	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	1166127	SO:0001162	SO:0001203	MTE	SO:0000167
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	1166128	SO:0001163	SO:0001683	INR1_motif	SO:0001411
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	1166129	SO:0001163	SO:0000167	INR1_motif	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	1166130	SO:0001164	SO:0000714	DPE1_motif	SO:0001683
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	1166131	SO:0001164	SO:0000167	DPE1_motif	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	1166132	SO:0001165	SO:0000714	DMv1_motif	SO:0001683
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	1166133	SO:0001165	SO:0000167	DMv1_motif	SO:0001055
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	1166134	SO:0001166	SO:0001683	GAGA_motif	SO:0001411
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	1166135	SO:0001166	SO:0000167	GAGA_motif	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	1166136	SO:0001167	SO:0000714	NDM2_motif	SO:0001683
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	1166137	SO:0001167	SO:0000167	NDM2_motif	SO:0001055
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	1166138	SO:0001168	SO:0000714	NDM3_motif	SO:0001683
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	1166139	SO:0001168	SO:0000167	NDM3_motif	SO:0001055
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	1166140	SO:0001169	SO:0001037	ds_RNA_viral_sequence	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	1166141	SO:0001169	SO:0001037	ds_RNA_viral_sequence	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	1640848	SO:0001169	SO:0001411	ds_RNA_viral_sequence	SO:0000001
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	1166143	SO:0001170	SO:0000101	polinton	SO:0001039
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	1166144	SO:0001171	SO:0000655	rRNA_21S	SO:0000233
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	1640853	SO:0001172	SO:0000673	tRNA_region	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	2279448	SO:0001172	SO:0001411	tRNA_region	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	1166147	SO:0001172	SO:0000233	tRNA_region	SO:0000673
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	1166148	SO:0001173	SO:0000655	anticodon_loop	SO:0000233
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	1166149	SO:0001173	SO:0000833	anticodon_loop	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	1166150	SO:0001173	SO:0000833	anticodon_loop	SO:0001411
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	1259943	SO:0001174	SO:0000655	anticodon	SO:0000233
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	1259944	SO:0001174	SO:0000833	anticodon	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	1259945	SO:0001174	SO:0000833	anticodon	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	1166154	SO:0001175	SO:0000655	CCA_tail	SO:0000233
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	1166155	SO:0001175	SO:0000833	CCA_tail	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	1166156	SO:0001175	SO:0000833	CCA_tail	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	1166157	SO:0001176	SO:0000655	DHU_loop	SO:0000233
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	1166158	SO:0001176	SO:0000833	DHU_loop	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	1166159	SO:0001176	SO:0000833	DHU_loop	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	1166160	SO:0001177	SO:0000655	T_loop	SO:0000233
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	1166161	SO:0001177	SO:0000833	T_loop	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	1166162	SO:0001177	SO:0000833	T_loop	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	1166163	SO:0001178	SO:0000185	pyrrolysine_tRNA_primary_transcript	SO:0000673
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	1166164	SO:0001179	SO:0000655	U3_snoRNA	SO:0000233
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	1259946	SO:0001180	SO:0000234	AU_rich_element	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	1259947	SO:0001180	SO:0000834	AU_rich_element	SO:0000833
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	1259948	SO:0001181	SO:0000234	Bruno_response_element	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	1259949	SO:0001181	SO:0000834	Bruno_response_element	SO:0000833
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	1166173	SO:0001182	SO:0000234	iron_responsive_element	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	1166174	SO:0001182	SO:0000834	iron_responsive_element	SO:0000833
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	1166175	SO:0001187	SO:0000655	pseudouridylation_guide_snoRNA	SO:0000233
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An oligo composed of LNA residues." [RSC:cb]	SO	1166176	SO:0001189	SO:0000695	LNA_oligo	SO:0001409
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An oligo composed of TNA residues." [RSC:cb]	SO	1166177	SO:0001191	SO:0000695	TNA_oligo	SO:0001409
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An oligo composed of GNA residues." [RSC:cb]	SO	1166178	SO:0001193	SO:0000695	GNA_oligo	SO:0001409
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]	SO	1166179	SO:0001194	SO:0000443	R_GNA	SO:0000400
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An oligo composed of (R)-GNA residues." [RSC:cb]	SO	1166180	SO:0001195	SO:0000696	R_GNA_oligo	SO:0000695
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]	SO	1166181	SO:0001196	SO:0000443	S_GNA	SO:0000400
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An oligo composed of (S)-GNA residues." [RSC:cb]	SO	1166182	SO:0001197	SO:0000696	S_GNA_oligo	SO:0000695
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	1166183	SO:0001198	SO:0001037	ds_DNA_viral_sequence	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	1166184	SO:0001198	SO:0001037	ds_DNA_viral_sequence	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	1640887	SO:0001198	SO:0001411	ds_DNA_viral_sequence	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	1166186	SO:0001199	SO:0001037	ss_RNA_viral_sequence	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	1166187	SO:0001199	SO:0001037	ss_RNA_viral_sequence	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	1640889	SO:0001199	SO:0001411	ss_RNA_viral_sequence	SO:0000001
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	1166189	SO:0001200	SO:0001038	negative_sense_ssRNA_viral_sequence	SO:0001037
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	1166190	SO:0001200	SO:0001235	negative_sense_ssRNA_viral_sequence	SO:0001411
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	1166191	SO:0001201	SO:0001038	positive_sense_ssRNA_viral_sequence	SO:0001037
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	1166192	SO:0001201	SO:0001235	positive_sense_ssRNA_viral_sequence	SO:0001411
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	\N	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	1166193	SO:0001202	SO:0001038	ambisense_ssRNA_viral_sequence	SO:0001037
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	1166194	SO:0001202	SO:0001235	ambisense_ssRNA_viral_sequence	SO:0001411
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1166195	SO:0001203	SO:0001679	RNA_polymerase_promoter	SO:0005836
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1166196	SO:0001204	SO:0001055	Phage_RNA_Polymerase_Promoter	SO:0001679
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1166197	SO:0001205	SO:0000167	SP6_RNA_Polymerase_Promoter	SO:0001055
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1166198	SO:0001206	SO:0000167	T3_RNA_Polymerase_Promoter	SO:0001055
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1166199	SO:0001207	SO:0000167	T7_RNA_Polymerase_Promoter	SO:0001055
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	1166200	SO:0001208	SO:0000696	five_prime_EST	SO:0000695
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	1166201	SO:0001209	SO:0000696	three_prime_EST	SO:0000695
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1166202	SO:0001210	SO:0000233	translational_frameshift	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1166203	SO:0001210	SO:0000833	translational_frameshift	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1166204	SO:0001210	SO:0000833	translational_frameshift	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1166205	SO:0001211	SO:0000234	plus_1_translational_frameshift	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1166206	SO:0001211	SO:0000834	plus_1_translational_frameshift	SO:0000833
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1166207	SO:0001212	SO:0000234	plus_2_translational_frameshift	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1166208	SO:0001212	SO:0000834	plus_2_translational_frameshift	SO:0000833
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	1166209	SO:0001213	SO:0000835	group_III_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	1166210	SO:0001213	SO:0000835	group_III_intron	SO:0000833
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	1259950	SO:0001214	SO:0000673	noncoding_region_of_exon	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	2279463	SO:0001214	SO:0001411	noncoding_region_of_exon	SO:0000001
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	1259952	SO:0001215	SO:0000673	coding_region_of_exon	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	2279464	SO:0001215	SO:0001411	coding_region_of_exon	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1166219	SO:0001216	SO:0000185	endonuclease_spliced_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1166220	SO:0001216	SO:0000833	endonuclease_spliced_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1166221	SO:0001216	SO:0000833	endonuclease_spliced_intron	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1166222	SO:0001217	SO:0000001	protein_coding_gene	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]	SO	1166223	SO:0001218	SO:0000001	transgenic_insertion	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1166224	SO:0001219	SO:0000001	retrogene	SO:0000110
4	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	SO	1166225	SO:0001220	SO:0000123	silenced_by_RNA_interference	SO:0000119
4	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	SO	1166226	SO:0001221	SO:0000123	silenced_by_histone_modification	SO:0000119
4	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	1166227	SO:0001222	SO:0000126	silenced_by_histone_methylation	SO:0000123
4	"An attribute describing a gene that is regulated at transcription." [SO:ma]	\N	transcriptionally_regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	1166228	SO:0001223	SO:0000126	silenced_by_histone_deacetylation	SO:0000123
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is silenced by RNA interference." [SO:xp]	SO	1166229	SO:0001224	SO:0001411	gene_silenced_by_RNA_interference	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is silenced by histone modification." [SO:xp]	SO	1166230	SO:0001225	SO:0001411	gene_silenced_by_histone_modification	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is silenced by histone methylation." [SO:xp]	SO	1166231	SO:0001226	SO:0000704	gene_silenced_by_histone_methylation	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene that is silenced by histone deacetylation." [SO:xp]	SO	1166232	SO:0001227	SO:0000704	gene_silenced_by_histone_deacetylation	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]	SO	1166233	SO:0001228	SO:0001236	dihydrouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]	SO	1166234	SO:0001229	SO:0001236	pseudouridine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	SO	1166235	SO:0001230	SO:0001411	inosine	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]	SO	1166236	SO:0001231	SO:0001411	seven_methylguanine	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]	SO	1166237	SO:0001232	SO:0001411	ribothymidine	SO:0000001
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	SO	1166238	SO:0001233	SO:0000250	methylinosine	SO:0001236
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1166239	SO:0001238	SO:0000185	major_TSS	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1166240	SO:0001238	SO:0000833	major_TSS	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1166241	SO:0001238	SO:0000833	major_TSS	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1166242	SO:0001239	SO:0000185	minor_TSS	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1166243	SO:0001239	SO:0000833	minor_TSS	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1166244	SO:0001239	SO:0000833	minor_TSS	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]	SO	1259954	SO:0001240	SO:0000001	TSS_region	SO:0000110
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	1166247	SO:0001243	SO:0000673	miRNA_primary_transcript_region	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	2081825	SO:0001243	SO:0001411	miRNA_primary_transcript_region	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	1166249	SO:0001244	SO:0000185	pre_miRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	1166250	SO:0001244	SO:0000833	pre_miRNA	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	1166251	SO:0001244	SO:0000833	pre_miRNA	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1259955	SO:0001245	SO:0000185	miRNA_stem	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1259956	SO:0001245	SO:0000833	miRNA_stem	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1259957	SO:0001245	SO:0000833	miRNA_stem	SO:0001411
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1166255	SO:0001245	SO:0000483	miRNA_stem	SO:0000185
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1259958	SO:0001246	SO:0000185	miRNA_loop	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1259959	SO:0001246	SO:0000833	miRNA_loop	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1259960	SO:0001246	SO:0000833	miRNA_loop	SO:0001411
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1166259	SO:0001246	SO:0000483	miRNA_loop	SO:0000185
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An oligo composed of synthetic nucleotides." [SO:ke]	SO	1166260	SO:0001247	SO:0001409	synthetic_oligo	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]	SO	1166261	SO:0001249	SO:0000001	fragment_assembly	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]	SO	1166262	SO:0001250	SO:0001410	fingerprint_map	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An STS map is a physical map organized by the unique STS landmarks." [SO:ke]	SO	1166263	SO:0001251	SO:0001410	STS_map	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A radiation hybrid map is a physical map." [SO:ke]	SO	1166264	SO:0001252	SO:0001410	RH_map	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]	SO	1166265	SO:0001253	SO:0000001	sonicate_fragment	SO:0000110
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	1166266	SO:0001254	SO:0001507	polyploid	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	1166267	SO:0001254	SO:0001524	polyploid	SO:0001506
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	1166268	SO:0001255	SO:0000240	autopolyploid	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	1166269	SO:0001255	SO:0000240	autopolyploid	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	1166270	SO:0001256	SO:0000240	allopolyploid	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	1166271	SO:0001256	SO:0000240	allopolyploid	SO:0001524
4	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	SO	1166272	SO:0001257	SO:0000410	homing_endonuclease_binding_site	SO:0000409
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	1166273	SO:0001258	SO:0001683	octamer_motif	SO:0001411
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	1166274	SO:0001258	SO:0000167	octamer_motif	SO:0001055
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A chromosome originating in an apicoplast." [SO:xp]	SO	1166275	SO:0001259	SO:0001411	apicoplast_chromosome	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]	SO	1166276	SO:0001261	SO:0001410	overlapping_feature_set	SO:0000001
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]	SO	1166277	SO:0001262	SO:0000700	overlapping_EST_set	SO:0001410
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1166278	SO:0001263	SO:0000001	ncRNA_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166279	SO:0001264	SO:0001411	gRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166280	SO:0001265	SO:0001411	miRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166281	SO:0001266	SO:0001411	scRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166282	SO:0001267	SO:0001411	snoRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166283	SO:0001268	SO:0001411	snRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166284	SO:0001269	SO:0001411	SRP_RNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166285	SO:0001270	SO:0001411	stRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166286	SO:0001271	SO:0001411	tmRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166287	SO:0001272	SO:0001411	tRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	SO	1166288	SO:0001273	SO:0001411	modified_adenosine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	SO	1166289	SO:0001274	SO:0001236	modified_inosine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	SO	1166290	SO:0001275	SO:0001411	modified_cytidine	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166291	SO:0001276	SO:0001411	modified_guanosine	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166292	SO:0001277	SO:0001411	modified_uridine	SO:0000001
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	1166293	SO:0001278	SO:0000250	one_methylinosine	SO:0001236
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	1166294	SO:0001279	SO:0000250	one_two_prime_O_dimethylinosine	SO:0001236
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	1166295	SO:0001280	SO:0000250	two_prime_O_methylinosine	SO:0001236
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166296	SO:0001281	SO:0001236	three_methylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166297	SO:0001282	SO:0001236	five_methylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166298	SO:0001283	SO:0001236	two_prime_O_methylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166299	SO:0001284	SO:0001236	two_thiocytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166300	SO:0001285	SO:0001236	N4_acetylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166301	SO:0001286	SO:0001236	five_formylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166302	SO:0001287	SO:0001236	five_two_prime_O_dimethylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166303	SO:0001288	SO:0001236	N4_acetyl_2_prime_O_methylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166304	SO:0001289	SO:0001236	lysidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166305	SO:0001290	SO:0001236	N4_methylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166306	SO:0001291	SO:0001236	N4_2_prime_O_dimethylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166307	SO:0001292	SO:0001236	five_hydroxymethylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166308	SO:0001293	SO:0001236	five_formyl_two_prime_O_methylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1166309	SO:0001294	SO:0001236	N4_N4_2_prime_O_trimethylcytidine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166310	SO:0001295	SO:0001236	one_methyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166311	SO:0001296	SO:0001236	two_methyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166312	SO:0001297	SO:0001236	N6_methyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166313	SO:0001298	SO:0001236	two_prime_O_methyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166314	SO:0001299	SO:0001236	two_methylthio_N6_methyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166315	SO:0001300	SO:0001236	N6_isopentenyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166316	SO:0001301	SO:0001236	two_methylthio_N6_isopentenyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166317	SO:0001302	SO:0001236	N6_cis_hydroxyisopentenyl_adenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166318	SO:0001303	SO:0001236	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166319	SO:0001304	SO:0001236	N6_glycinylcarbamoyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166320	SO:0001305	SO:0001236	N6_threonylcarbamoyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166321	SO:0001306	SO:0001236	two_methylthio_N6_threonyl_carbamoyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166322	SO:0001307	SO:0001236	N6_methyl_N6_threonylcarbamoyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166323	SO:0001308	SO:0001236	N6_hydroxynorvalylcarbamoyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166324	SO:0001309	SO:0001236	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166325	SO:0001310	SO:0001236	two_prime_O_ribosyladenosine_phosphate	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166326	SO:0001311	SO:0001236	N6_N6_dimethyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166327	SO:0001312	SO:0001236	N6_2_prime_O_dimethyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166328	SO:0001313	SO:0001236	N6_N6_2_prime_O_trimethyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166329	SO:0001314	SO:0001236	one_two_prime_O_dimethyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1166330	SO:0001315	SO:0001236	N6_acetyladenosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	SO	1166331	SO:0001316	SO:0001236	seven_deazaguanosine	SO:0001411
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1166332	SO:0001317	SO:0000250	queuosine	SO:0001236
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1166333	SO:0001318	SO:0000250	epoxyqueuosine	SO:0001236
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1166334	SO:0001319	SO:0000250	galactosyl_queuosine	SO:0001236
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1166335	SO:0001320	SO:0000250	mannosyl_queuosine	SO:0001236
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1166336	SO:0001321	SO:0000250	seven_cyano_seven_deazaguanosine	SO:0001236
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1166337	SO:0001322	SO:0000250	seven_aminomethyl_seven_deazaguanosine	SO:0001236
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	\N	sequence	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1166338	SO:0001323	SO:0000250	archaeosine	SO:0001236
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166339	SO:0001324	SO:0001236	one_methylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166340	SO:0001325	SO:0001236	N2_methylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166341	SO:0001326	SO:0001236	seven_methylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166342	SO:0001327	SO:0001236	two_prime_O_methylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166343	SO:0001328	SO:0001236	N2_N2_dimethylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166344	SO:0001329	SO:0001236	N2_2_prime_O_dimethylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166345	SO:0001330	SO:0001236	N2_N2_2_prime_O_trimethylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166346	SO:0001331	SO:0001236	two_prime_O_ribosylguanosine_phosphate	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166347	SO:0001332	SO:0001236	wybutosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166348	SO:0001333	SO:0001236	peroxywybutosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166349	SO:0001334	SO:0001236	hydroxywybutosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166350	SO:0001335	SO:0001236	undermodified_hydroxywybutosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166351	SO:0001336	SO:0001236	wyosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166352	SO:0001337	SO:0001236	methylwyosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166353	SO:0001338	SO:0001236	N2_7_dimethylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166354	SO:0001339	SO:0001236	N2_N2_7_trimethylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166355	SO:0001340	SO:0001236	one_two_prime_O_dimethylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166356	SO:0001341	SO:0001236	four_demethylwyosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166357	SO:0001342	SO:0001236	isowyosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166358	SO:0001343	SO:0001236	N2_7_2prirme_O_trimethylguanosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166359	SO:0001344	SO:0001236	five_methyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166360	SO:0001345	SO:0001236	two_prime_O_methyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166361	SO:0001346	SO:0001236	five_two_prime_O_dimethyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166362	SO:0001347	SO:0001236	one_methylpseudouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166363	SO:0001348	SO:0001236	two_prime_O_methylpseudouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166364	SO:0001349	SO:0001236	two_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166365	SO:0001350	SO:0001236	four_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166366	SO:0001351	SO:0001236	five_methyl_2_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166367	SO:0001352	SO:0001236	two_thio_two_prime_O_methyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166368	SO:0001353	SO:0001236	three_three_amino_three_carboxypropyl_uridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166369	SO:0001354	SO:0001236	five_hydroxyuridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166370	SO:0001355	SO:0001236	five_methoxyuridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166371	SO:0001356	SO:0001236	uridine_five_oxyacetic_acid	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166372	SO:0001357	SO:0001236	uridine_five_oxyacetic_acid_methyl_ester	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166373	SO:0001358	SO:0001236	five_carboxyhydroxymethyl_uridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166374	SO:0001359	SO:0001236	five_carboxyhydroxymethyl_uridine_methyl_ester	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166375	SO:0001360	SO:0001236	five_methoxycarbonylmethyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166376	SO:0001361	SO:0001236	five_methoxycarbonylmethyl_two_prime_O_methyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166377	SO:0001362	SO:0001236	five_methoxycarbonylmethyl_two_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166378	SO:0001363	SO:0001236	five_aminomethyl_two_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166379	SO:0001364	SO:0001236	five_methylaminomethyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166380	SO:0001365	SO:0001236	five_methylaminomethyl_two_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166381	SO:0001366	SO:0001236	five_methylaminomethyl_two_selenouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166382	SO:0001367	SO:0001236	five_carbamoylmethyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166383	SO:0001368	SO:0001236	five_carbamoylmethyl_two_prime_O_methyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166384	SO:0001369	SO:0001236	five_carboxymethylaminomethyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166385	SO:0001370	SO:0001236	five_carboxymethylaminomethyl_two_prime_O_methyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166386	SO:0001371	SO:0001236	five_carboxymethylaminomethyl_two_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166387	SO:0001372	SO:0001236	three_methyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166388	SO:0001373	SO:0001236	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166389	SO:0001374	SO:0001236	five_carboxymethyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166390	SO:0001375	SO:0001236	three_two_prime_O_dimethyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166391	SO:0001376	SO:0001236	five_methyldihydrouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166392	SO:0001377	SO:0001236	three_methylpseudouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166393	SO:0001378	SO:0001236	five_taurinomethyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166394	SO:0001379	SO:0001236	five_taurinomethyl_two_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166395	SO:0001380	SO:0001236	five_isopentenylaminomethyl_uridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166396	SO:0001381	SO:0001236	five_isopentenylaminomethyl_two_thiouridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1166397	SO:0001382	SO:0001236	five_isopentenylaminomethyl_two_prime_O_methyluridine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]	SO	1166398	SO:0001383	SO:0000409	histone_binding_site	SO:0001411
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"" []	SO	1166399	SO:0001384	SO:0000234	CDS_fragment	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	1166400	SO:0001384	SO:0000834	CDS_fragment	SO:0000833
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified amino acid feature." [SO:ke]	SO	1259961	SO:0001385	SO:0000001	modified_amino_acid_feature	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified glycine amino acid feature." [SO:ke]	SO	1166403	SO:0001386	SO:0000104	modified_glycine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified glycine amino acid feature." [SO:ke]	SO	1641087	SO:0001386	SO:0001411	modified_glycine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified alanine amino acid feature." [SO:ke]	SO	1166405	SO:0001387	SO:0000104	modified_L_alanine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified alanine amino acid feature." [SO:ke]	SO	1641089	SO:0001387	SO:0001411	modified_L_alanine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified asparagine amino acid feature." [SO:ke]	SO	1166407	SO:0001388	SO:0000104	modified_L_asparagine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified asparagine amino acid feature." [SO:ke]	SO	1641091	SO:0001388	SO:0001411	modified_L_asparagine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	SO	1166409	SO:0001389	SO:0000104	modified_L_aspartic_acid	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	SO	1641093	SO:0001389	SO:0001411	modified_L_aspartic_acid	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified cysteine amino acid feature." [SO:ke]	SO	1166411	SO:0001390	SO:0000104	modified_L_cysteine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified cysteine amino acid feature." [SO:ke]	SO	1641095	SO:0001390	SO:0001411	modified_L_cysteine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1166413	SO:0001391	SO:0000104	modified_L_glutamic_acid	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1641097	SO:0001391	SO:0001411	modified_L_glutamic_acid	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified threonine amino acid feature." [SO:ke]	SO	1166415	SO:0001392	SO:0000104	modified_L_threonine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified threonine amino acid feature." [SO:ke]	SO	1641099	SO:0001392	SO:0001411	modified_L_threonine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified tryptophan amino acid feature." [SO:ke]	SO	1166417	SO:0001393	SO:0000104	modified_L_tryptophan	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified tryptophan amino acid feature." [SO:ke]	SO	1641101	SO:0001393	SO:0001411	modified_L_tryptophan	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified glutamine amino acid feature." [SO:ke]	SO	1166419	SO:0001394	SO:0000104	modified_L_glutamine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified glutamine amino acid feature." [SO:ke]	SO	1641103	SO:0001394	SO:0001411	modified_L_glutamine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified methionine amino acid feature." [SO:ke]	SO	1166421	SO:0001395	SO:0000104	modified_L_methionine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified methionine amino acid feature." [SO:ke]	SO	1641105	SO:0001395	SO:0001411	modified_L_methionine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified isoleucine amino acid feature." [SO:ke]	SO	1166423	SO:0001396	SO:0000104	modified_L_isoleucine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified isoleucine amino acid feature." [SO:ke]	SO	1641107	SO:0001396	SO:0001411	modified_L_isoleucine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	SO	1166425	SO:0001397	SO:0000104	modified_L_phenylalanine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	SO	1641109	SO:0001397	SO:0001411	modified_L_phenylalanine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified histidine amino acid feature." [SO:ke]	SO	1166427	SO:0001398	SO:0000104	modified_L_histidine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified histidine amino acid feature." [SO:ke]	SO	1641111	SO:0001398	SO:0001411	modified_L_histidine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified serine amino acid feature." [SO:ke]	SO	1166429	SO:0001399	SO:0000104	modified_L_serine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified serine amino acid feature." [SO:ke]	SO	1641113	SO:0001399	SO:0001411	modified_L_serine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified lysine amino acid feature." [SO:ke]	SO	1166431	SO:0001400	SO:0000104	modified_L_lysine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified lysine amino acid feature." [SO:ke]	SO	1641115	SO:0001400	SO:0001411	modified_L_lysine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified leucine amino acid feature." [SO:ke]	SO	1166433	SO:0001401	SO:0000104	modified_L_leucine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified leucine amino acid feature." [SO:ke]	SO	1641117	SO:0001401	SO:0001411	modified_L_leucine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	SO	1166435	SO:0001402	SO:0000104	modified_L_selenocysteine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	SO	1641119	SO:0001402	SO:0001411	modified_L_selenocysteine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified valine amino acid feature." [SO:ke]	SO	1166437	SO:0001403	SO:0000104	modified_L_valine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified valine amino acid feature." [SO:ke]	SO	1641121	SO:0001403	SO:0001411	modified_L_valine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified proline amino acid feature." [SO:ke]	SO	1166439	SO:0001404	SO:0000104	modified_L_proline	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified proline amino acid feature." [SO:ke]	SO	1641123	SO:0001404	SO:0001411	modified_L_proline	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified tyrosine amino acid feature." [SO:ke]	SO	1166441	SO:0001405	SO:0000104	modified_L_tyrosine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified tyrosine amino acid feature." [SO:ke]	SO	1641125	SO:0001405	SO:0001411	modified_L_tyrosine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post translationally modified arginine amino acid feature." [SO:ke]	SO	1166443	SO:0001406	SO:0000104	modified_L_arginine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post translationally modified arginine amino acid feature." [SO:ke]	SO	1641127	SO:0001406	SO:0001411	modified_L_arginine	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	1259962	SO:0001408	SO:0000104	cleaved_for_gpi_anchor_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	1805730	SO:0001408	SO:0001411	cleaved_for_gpi_anchor_region	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	1166449	SO:0001413	SO:0001235	translocation_breakpoint	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	1166450	SO:0001414	SO:0001235	insertion_breakpoint	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	1166451	SO:0001415	SO:0001235	deletion_breakpoint	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A flanking region located five prime of a specific region." [SO:chado]	SO	1166452	SO:0001416	SO:0000001	five_prime_flanking_region	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A flanking region located three prime of a specific region." [SO:chado]	SO	1166453	SO:0001417	SO:0000001	three_prime_flanking_region	SO:0000110
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	1166454	SO:0001419	SO:0000185	cis_splice_site	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	1166455	SO:0001419	SO:0000833	cis_splice_site	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	1166456	SO:0001419	SO:0000833	cis_splice_site	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	1166457	SO:0001420	SO:0000185	trans_splice_site	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	1166458	SO:0001420	SO:0000833	trans_splice_site	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	1166459	SO:0001420	SO:0000833	trans_splice_site	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	1166460	SO:0001422	SO:0100021	conformational_switch	SO:0000839
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	2764379	SO:0001423	SO:0001410	dye_terminator_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	1166463	SO:0001423	SO:0000148	dye_terminator_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	1166464	SO:0001423	SO:0000148	dye_terminator_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	2279469	SO:0001423	SO:0000353	dye_terminator_read	SO:0001248
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	2764380	SO:0001424	SO:0001410	pyrosequenced_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	1166468	SO:0001424	SO:0000148	pyrosequenced_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	1166469	SO:0001424	SO:0000148	pyrosequenced_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	2279470	SO:0001424	SO:0000353	pyrosequenced_read	SO:0001248
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	2764381	SO:0001425	SO:0001410	ligation_based_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	1166473	SO:0001425	SO:0000148	ligation_based_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	1166474	SO:0001425	SO:0000148	ligation_based_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	2279471	SO:0001425	SO:0000353	ligation_based_read	SO:0001248
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	2764382	SO:0001426	SO:0001410	polymerase_synthesis_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	1166478	SO:0001426	SO:0000148	polymerase_synthesis_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	1166479	SO:0001426	SO:0000148	polymerase_synthesis_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	2279472	SO:0001426	SO:0000353	polymerase_synthesis_read	SO:0001248
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]	SO	1166481	SO:0001427	SO:0000831	cis_regulatory_frameshift_element	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence assembly derived from expressed sequences." [SO:ke]	SO	1166482	SO:0001428	SO:0001410	expressed_sequence_assembly	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	SO	1166483	SO:0001429	SO:0001411	DNA_binding_site	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]	SO	1166484	SO:0001431	SO:0000001	cryptic_gene	SO:0000110
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]	SO	1166485	SO:0001433	SO:0000695	three_prime_RACE_clone	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]	SO	1166486	SO:0001434	SO:0001411	cassette_pseudogene	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259968	SO:0001435	SO:0000001	alanine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259969	SO:0001436	SO:0000001	valine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259970	SO:0001437	SO:0000001	leucine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259971	SO:0001438	SO:0000001	isoleucine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259972	SO:0001439	SO:0000001	proline	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259973	SO:0001440	SO:0000001	tryptophan	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259974	SO:0001441	SO:0000001	phenylalanine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259975	SO:0001442	SO:0000001	methionine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259976	SO:0001443	SO:0000001	glycine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259977	SO:0001444	SO:0000001	serine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259978	SO:0001445	SO:0000001	threonine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259979	SO:0001446	SO:0000001	tyrosine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259980	SO:0001447	SO:0000001	cysteine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259981	SO:0001448	SO:0000001	glutamine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259982	SO:0001449	SO:0000001	asparagine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259983	SO:0001450	SO:0000001	lysine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259984	SO:0001451	SO:0000001	arginine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259985	SO:0001452	SO:0000001	histidine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259986	SO:0001453	SO:0000001	aspartic_acid	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259987	SO:0001454	SO:0000001	glutamic_acid	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259988	SO:0001455	SO:0000001	selenocysteine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1259989	SO:0001456	SO:0000001	pyrrolysine	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]	SO	1166531	SO:0001458	SO:0000001	unigene_cluster	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]	SO	1166532	SO:0001459	SO:0001411	CRISPR	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	1166533	SO:0001460	SO:0000409	insulator_binding_site	SO:0001411
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	1166534	SO:0001460	SO:0001679	insulator_binding_site	SO:0005836
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	1166535	SO:0001461	SO:0000409	enhancer_binding_site	SO:0001411
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	1166536	SO:0001461	SO:0001055	enhancer_binding_site	SO:0001679
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A collection of contigs." [SO:ke]	SO	1166537	SO:0001462	SO:0000700	contig_collection	SO:0001410
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	1166538	SO:0001463	SO:0000233	lincRNA	SO:0000673
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	SO	1166539	SO:0001464	SO:0000696	UST	SO:0000695
4	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	1166540	SO:0001465	SO:0000324	three_prime_UST	SO:0000696
4	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	1166541	SO:0001466	SO:0000324	five_prime_UST	SO:0000696
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	1166542	SO:0001467	SO:0000696	RST	SO:0000695
4	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	1166543	SO:0001468	SO:0000324	three_prime_RST	SO:0000696
4	"A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]	\N	oligo	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	1166544	SO:0001469	SO:0000324	five_prime_RST	SO:0000696
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A match against an UST sequence." [SO:nlw]	SO	1166545	SO:0001470	SO:0000343	UST_match	SO:0001410
4	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A match against an RST sequence." [SO:nlw]	SO	1166546	SO:0001471	SO:0000343	RST_match	SO:0001410
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A nucleotide match to a primer sequence." [SO:nlw]	SO	1166547	SO:0001472	SO:0001410	primer_match	SO:0000001
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	1166548	SO:0001473	SO:0000185	miRNA_antiguide	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	1166549	SO:0001473	SO:0000833	miRNA_antiguide	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	1166550	SO:0001473	SO:0000833	miRNA_antiguide	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	1166551	SO:0001475	SO:0000673	outron	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	2081987	SO:0001475	SO:0001411	outron	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	1166553	SO:0001476	SO:0001411	natural_plasmid	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A plasmid that occurs naturally." [SO:xp]	SO	1641180	SO:0001476	SO:0000001	natural_plasmid	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	1166555	SO:0001477	SO:0001235	gene_trap_construct	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	2081988	SO:0001477	SO:0000001	gene_trap_construct	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	1166557	SO:0001477	SO:0001409	gene_trap_construct	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	1166558	SO:0001478	SO:0001235	promoter_trap_construct	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	2081989	SO:0001478	SO:0000001	promoter_trap_construct	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	1166560	SO:0001478	SO:0001409	promoter_trap_construct	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	1166561	SO:0001479	SO:0001235	enhancer_trap_construct	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	2081990	SO:0001479	SO:0000001	enhancer_trap_construct	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	1166563	SO:0001479	SO:0001409	enhancer_trap_construct	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	2764384	SO:0001480	SO:0001410	PAC_end	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	1166566	SO:0001480	SO:0000148	PAC_end	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	1166567	SO:0001480	SO:0000148	PAC_end	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	2279473	SO:0001480	SO:0000353	PAC_end	SO:0001248
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	1166569	SO:0001480	SO:0000151	PAC_end	SO:0000695
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	1166570	SO:0001480	SO:0001235	PAC_end	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]	SO	1166571	SO:0001481	SO:0001409	RAPD	SO:0000001
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1166572	SO:0001482	SO:0001055	shadow_enhancer	SO:0001679
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	SO	1166573	SO:0001483	SO:0000001	SNV	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	2452731	SO:0001484	SO:0000001	X_element_combinatorial_repeat	SO:0000110
4	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	1166575	SO:0001484	SO:0000830	X_element_combinatorial_repeat	SO:0000340
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	1166576	SO:0001484	SO:0000830	X_element_combinatorial_repeat	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	2452732	SO:0001485	SO:0000001	Y_prime_element	SO:0000110
4	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	1166578	SO:0001485	SO:0000830	Y_prime_element	SO:0000340
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	1166579	SO:0001485	SO:0000830	Y_prime_element	SO:0001411
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]	SO	1166580	SO:0001486	SO:0000733	standard_draft	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]	SO	1166581	SO:0001487	SO:0000733	high_quality_draft	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]	SO	1166582	SO:0001488	SO:0000733	improved_high_quality_draft	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]	SO	1166583	SO:0001489	SO:0000733	annotation_directed_improved_draft	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]	SO	1166584	SO:0001490	SO:0000733	noncontiguous_finished	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]	SO	1166585	SO:0001491	SO:0000733	finished_genome	SO:0000400
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	2081999	SO:0001492	SO:0000831	intronic_regulatory_region	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	1166587	SO:0001492	SO:0000185	intronic_regulatory_region	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	1166588	SO:0001492	SO:0000833	intronic_regulatory_region	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	1166589	SO:0001492	SO:0000833	intronic_regulatory_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	2806647	SO:0001493	SO:0000001	centromere_DNA_Element_I	SO:0000110
4	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	1166591	SO:0001493	SO:0000628	centromere_DNA_Element_I	SO:0000830
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	2806648	SO:0001494	SO:0000001	centromere_DNA_Element_II	SO:0000110
4	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	1166593	SO:0001494	SO:0000628	centromere_DNA_Element_II	SO:0000830
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	2806649	SO:0001495	SO:0000001	centromere_DNA_Element_III	SO:0000110
4	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	1166595	SO:0001495	SO:0000628	centromere_DNA_Element_III	SO:0000830
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	2452733	SO:0001496	SO:0000001	telomeric_repeat	SO:0000110
4	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	1166597	SO:0001496	SO:0000830	telomeric_repeat	SO:0000340
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	1166598	SO:0001496	SO:0000830	telomeric_repeat	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	2548844	SO:0001497	SO:0000001	X_element	SO:0000110
4	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	1166600	SO:0001497	SO:0000830	X_element	SO:0000340
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	1166601	SO:0001497	SO:0000830	X_element	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	2764385	SO:0001498	SO:0001410	YAC_end	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	1166604	SO:0001498	SO:0000148	YAC_end	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	1166605	SO:0001498	SO:0000148	YAC_end	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	2279474	SO:0001498	SO:0000353	YAC_end	SO:0001248
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	1166607	SO:0001498	SO:0000151	YAC_end	SO:0000695
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	1166608	SO:0001498	SO:0001235	YAC_end	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]	SO	1166609	SO:0001500	SO:0000001	heritable_phenotypic_marker	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]	SO	1166610	SO:0001503	SO:0001411	processed_transcript	SO:0000001
4	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome variation derived from an event during meiosis." [SO:ke]	SO	1166611	SO:0001504	SO:0001506	assortment_derived_variation	SO:0001026
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1166612	SO:0001510	SO:0000733	intrachromosomal	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1166613	SO:0001511	SO:0000733	interchromosomal	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1166614	SO:0001513	SO:0000733	tandem	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]	SO	1166615	SO:0001514	SO:0000733	direct	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]	SO	1166616	SO:0001515	SO:0000733	inverted	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The quality of a duplication where the new region exists independently of the original." [SO:ke]	SO	1166617	SO:0001516	SO:0000733	free	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1166618	SO:0001518	SO:0000733	pericentric	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1166619	SO:0001519	SO:0000733	paracentric	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1166620	SO:0001521	SO:0000733	reciprocal	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1166621	SO:0001522	SO:0000733	insertional	SO:0000400
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]	SO	1166622	SO:0001525	SO:0001410	assembly_error_correction	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]	SO	1166623	SO:0001526	SO:0001410	base_call_error_correction	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]	SO	1259992	SO:0001527	SO:0000001	peptide_localization_signal	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	SO	1166626	SO:0001528	SO:0000104	nuclear_localization_signal	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	SO	1641221	SO:0001528	SO:0001411	nuclear_localization_signal	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	SO	1166628	SO:0001529	SO:0000104	endosomal_localization_signal	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	SO	1641223	SO:0001529	SO:0001411	endosomal_localization_signal	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	SO	1166630	SO:0001530	SO:0000104	lysosomal_localization_signal	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	SO	1641225	SO:0001530	SO:0001411	lysosomal_localization_signal	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	SO	1166632	SO:0001531	SO:0000104	nuclear_export_signal	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	SO	1641227	SO:0001531	SO:0001411	nuclear_export_signal	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region recognized by a recombinase." [SO:ke]	SO	1166634	SO:0001532	SO:0000298	recombination_signal_sequence	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	1166635	SO:0001533	SO:0000185	cryptic_splice_site	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	1166636	SO:0001533	SO:0000833	cryptic_splice_site	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	1166637	SO:0001533	SO:0000833	cryptic_splice_site	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	SO	1166638	SO:0001534	SO:0000104	nuclear_rim_localization_signal	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	SO	1641232	SO:0001534	SO:0001411	nuclear_rim_localization_signal	SO:0000001
4	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	1166640	SO:0001535	SO:0001039	p_element	SO:0001037
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	1166641	SO:0001541	SO:0001536	decreased_transcript_level_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]	SO	1166642	SO:0001542	SO:0001536	increased_transcript_level_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]	SO	1166643	SO:0001544	SO:0001536	editing_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]	SO	1166644	SO:0001545	SO:0001536	polyadenylation_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]	SO	1166645	SO:0001547	SO:0001536	decreased_transcript_stability_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]	SO	1166646	SO:0001548	SO:0001536	increased_transcript_stability_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]	SO	1166647	SO:0001550	SO:0001536	rate_of_transcription_variant	SO:0001060
4	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	1166648	SO:0001551	SO:0001538	increased_transcription_rate_variant	SO:0001536
4	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	1166649	SO:0001552	SO:0001538	decreased_transcription_rate_variant	SO:0001536
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]	SO	1166650	SO:0001555	SO:0001536	decreased_translational_product_level	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]	SO	1166651	SO:0001556	SO:0001536	increased_translational_product_level	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]	SO	1166652	SO:0001557	SO:0001536	polypeptide_gain_of_function_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]	SO	1166653	SO:0001558	SO:0001536	polypeptide_localization_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]	SO	1166654	SO:0001559	SO:0001536	polypeptide_loss_of_function_variant	SO:0001060
4	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]	SO	1166655	SO:0001560	SO:0001539	inactive_ligand_binding_site	SO:0001536
4	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]	SO	1166656	SO:0001561	SO:0001539	polypeptide_partial_loss_of_function	SO:0001536
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]	SO	1166657	SO:0001562	SO:0001536	polypeptide_post_translational_processing_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby a two genes have become joined." [SO:ke]	SO	1166658	SO:0001565	SO:0001537	gene_fusion	SO:0001060
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	1166659	SO:0001567	SO:0001791	stop_retained_variant	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	1166660	SO:0001567	SO:0001968	stop_retained_variant	SO:0001576
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that changes the process of splicing." [SO:ke]	SO	1166661	SO:0001568	SO:0001878	splicing_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1166662	SO:0001569	SO:0001564	cryptic_splice_site_variant	SO:0001878
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	SO	1166663	SO:0001570	SO:0001576	cryptic_splice_acceptor	SO:0001564
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	SO	1166664	SO:0001571	SO:0001576	cryptic_splice_donor	SO:0001564
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby an exon is lost from the transcript." [SO:ke]	SO	1166665	SO:0001572	SO:0001564	exon_loss_variant	SO:0001878
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1166666	SO:0001573	SO:0001564	intron_gain	SO:0001878
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	1166667	SO:0001574	SO:0001576	splice_acceptor_variant	SO:0001564
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	1166668	SO:0001575	SO:0001576	splice_donor_variant	SO:0001564
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes the structure of the transcript." [SO:ke]	SO	1166669	SO:0001576	SO:0001537	transcript_variant	SO:0001060
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]	SO	1166670	SO:0001577	SO:0001878	complex_transcript_variant	SO:0001537
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	1679603	SO:0001578	SO:0001791	stop_lost	SO:0001576
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	1679604	SO:0001578	SO:0001968	stop_lost	SO:0001576
10	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	2889310	SO:0001578	SO:0001537	stop_lost	SO:0001060
4	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	1166674	SO:0001578	SO:0001818	stop_lost	SO:0001580
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	1166675	SO:0001580	SO:0001564	coding_sequence_variant	SO:0001878
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	1166676	SO:0001582	SO:0001576	initiator_codon_variant	SO:0001564
4	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	1166677	SO:0001583	SO:0001818	missense_variant	SO:0001580
4	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	1166678	SO:0001585	SO:0001650	conservative_missense_variant	SO:0001818
4	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	1166679	SO:0001586	SO:0001650	non_conservative_missense_variant	SO:0001818
10	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	2889311	SO:0001587	SO:0001537	stop_gained	SO:0001060
4	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	1166681	SO:0001587	SO:0001818	stop_gained	SO:0001580
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	1166682	SO:0001589	SO:0001791	frameshift_variant	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	1166683	SO:0001589	SO:0001968	frameshift_variant	SO:0001576
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	1166684	SO:0001590	SO:0001576	terminator_codon_variant	SO:0001564
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	1166685	SO:0001591	SO:0001580	frame_restoring_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	1166686	SO:0001591	SO:0001580	frame_restoring_variant	SO:0001968
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	1166687	SO:0001592	SO:0001580	minus_1_frameshift_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	1166688	SO:0001592	SO:0001580	minus_1_frameshift_variant	SO:0001968
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"" []	SO	1166689	SO:0001593	SO:0001580	minus_2_frameshift_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"" []	SO	1166690	SO:0001593	SO:0001580	minus_2_frameshift_variant	SO:0001968
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	1166691	SO:0001594	SO:0001580	plus_1_frameshift_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	1166692	SO:0001594	SO:0001580	plus_1_frameshift_variant	SO:0001968
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"" []	SO	1166693	SO:0001595	SO:0001580	plus_2_frameshift_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"" []	SO	1166694	SO:0001595	SO:0001580	plus_2_frameshift_variant	SO:0001968
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]	SO	1166695	SO:0001596	SO:0001878	transcript_secondary_structure_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]	SO	1166696	SO:0001597	SO:0001564	compensatory_transcript_secondary_structure_variant	SO:0001878
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	SO	1166697	SO:0001598	SO:0001537	translational_product_structure_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes the resulting polypeptide structure." [SO:ke]	SO	1166698	SO:0001600	SO:0001536	complex_3D_structural_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]	SO	1166699	SO:0001601	SO:0001536	conformational_change_variant	SO:0001060
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	SO	1166700	SO:0001603	SO:0001878	polypeptide_sequence_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]	SO	1166701	SO:0001604	SO:0001564	amino_acid_deletion	SO:0001878
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]	SO	1166702	SO:0001605	SO:0001564	amino_acid_insertion	SO:0001878
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	SO	1166703	SO:0001606	SO:0001564	amino_acid_substitution	SO:0001878
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	SO	1166704	SO:0001607	SO:0001598	conservative_amino_acid_substitution	SO:0001564
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	SO	1166705	SO:0001608	SO:0001598	non_conservative_amino_acid_substitution	SO:0001564
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	SO	1166706	SO:0001609	SO:0001564	elongated_polypeptide	SO:0001878
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	1166707	SO:0001610	SO:0001598	elongated_polypeptide_C_terminal	SO:0001564
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	1166708	SO:0001611	SO:0001598	elongated_polypeptide_N_terminal	SO:0001564
4	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	1166709	SO:0001612	SO:0001603	elongated_in_frame_polypeptide_C_terminal	SO:0001598
4	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	1166710	SO:0001613	SO:0001603	elongated_out_of_frame_polypeptide_C_terminal	SO:0001598
4	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	1166711	SO:0001614	SO:0001603	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001598
4	"A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]	\N	translational_product_structure_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	1166712	SO:0001615	SO:0001603	elongated_out_of_frame_polypeptide_N_terminal	SO:0001598
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]	SO	1166713	SO:0001616	SO:0001564	polypeptide_fusion	SO:0001878
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]	SO	1166714	SO:0001617	SO:0001564	polypeptide_truncation	SO:0001878
4	"A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]	\N	translational_product_function_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]	SO	1166715	SO:0001618	SO:0001554	inactive_catalytic_site	SO:0001539
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant of a non coding RNA gene." [SO:ke]	SO	1166716	SO:0001619	SO:0001878	non_coding_transcript_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant located with the sequence of the mature miRNA." [SO:ke]	SO	1166717	SO:0001620	SO:0001564	mature_miRNA_variant	SO:0001878
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A variant in a transcript that is the target of NMD." [SO:ke]	SO	1166718	SO:0001621	SO:0001878	NMD_transcript_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	1166719	SO:0001622	SO:0001564	UTR_variant	SO:0001878
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	1166720	SO:0001623	SO:0001576	5_prime_UTR_variant	SO:0001564
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	1166721	SO:0001624	SO:0001576	3_prime_UTR_variant	SO:0001564
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	1259993	SO:0001626	SO:0001791	incomplete_terminal_codon_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	1259994	SO:0001626	SO:0001968	incomplete_terminal_codon_variant	SO:0001576
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant occurring within an intron." [SO:ke]	SO	1166726	SO:0001627	SO:0001878	intron_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	1166727	SO:0001629	SO:0001564	splice_site_variant	SO:0001878
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]	SO	1166728	SO:0001630	SO:0001564	splice_region_variant	SO:0001878
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located 5' of a gene." [SO:ke]	SO	1166729	SO:0001631	SO:0001537	upstream_gene_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located 3' of a gene." [SO:ke]	SO	1166730	SO:0001632	SO:0001537	downstream_gene_variant	SO:0001060
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located within 5 KB of the end of a gene." [SO:ke]	SO	1166731	SO:0001633	SO:0001878	5KB_downstream_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located within a half KB of the end of a gene." [SO:ke]	SO	1166732	SO:0001634	SO:0001628	500B_downstream_variant	SO:0001878
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located within 5KB 5' of a gene." [SO:ke]	SO	1166733	SO:0001635	SO:0001878	5KB_upstream_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant located within 2KB 5' of a gene." [SO:ke]	SO	1166734	SO:0001636	SO:0001628	2KB_upstream_variant	SO:0001878
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes for ribosomal RNA." [SO:ke]	SO	1166735	SO:0001637	SO:0001411	rRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes for an piwi associated RNA." [SO:ke]	SO	1166736	SO:0001638	SO:0001411	piRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes an RNase P RNA." [SO:ke]	SO	1166737	SO:0001639	SO:0001411	RNase_P_RNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes a RNase_MRP_RNA." [SO:ke]	SO	1166738	SO:0001640	SO:0001411	RNase_MRP_RNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes large intervening non-coding RNA." [SO:ke]	SO	1166739	SO:0001641	SO:0001411	lincRNA_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]	SO	1166740	SO:0001643	SO:0001411	telomerase_RNA_gene	SO:0000001
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	1166741	SO:0001644	SO:0000695	targeting_vector	SO:0001409
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]	SO	1166742	SO:0001644	SO:0001411	targeting_vector	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]	SO	1166744	SO:0001646	SO:0000001	DArT_marker	SO:0000110
4	"A region of an mRNA." [SO:cb]	SOFA	mRNA_region	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	1166745	SO:0001647	SO:0000203	kozak_sequence	SO:0000836
6	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	1679606	SO:0001647	SO:0000234	kozak_sequence	SO:0000233
6	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	1679607	SO:0001647	SO:0000834	kozak_sequence	SO:0000833
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposon that is disrupted by the insertion of another element." [SO:ke]	SO	1166748	SO:0001648	SO:0001037	nested_transposon	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposon that is disrupted by the insertion of another element." [SO:ke]	SO	1166749	SO:0001648	SO:0001037	nested_transposon	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A repeat that is disrupted by the insertion of another element." [SO:ke]	SO	1166750	SO:0001649	SO:0000001	nested_repeat	SO:0000110
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	1166751	SO:0001650	SO:0001791	inframe_variant	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	1166752	SO:0001650	SO:0001968	inframe_variant	SO:0001576
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	1166753	SO:0001653	SO:0001683	retinoic_acid_responsive_element	SO:0001411
4	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	1166754	SO:0001653	SO:0001679	retinoic_acid_responsive_element	SO:0005836
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	1166755	SO:0001654	SO:0001411	nucleotide_to_protein_binding_site	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]	SO	1166756	SO:0001655	SO:0000001	nucleotide_binding_site	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]	SO	1166757	SO:0001656	SO:0000001	metal_binding_site	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]	SO	1166758	SO:0001657	SO:0000001	ligand_binding_site	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]	SO	1166759	SO:0001658	SO:0001411	nested_tandem_repeat	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1166760	SO:0001659	SO:0001683	promoter_element	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"" []	SO	1166761	SO:0001660	SO:0000714	core_promoter_element	SO:0001683
4	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	1166762	SO:0001661	SO:0001659	RNA_polymerase_II_TATA_box	SO:0000713
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	1166763	SO:0001661	SO:0001203	RNA_polymerase_II_TATA_box	SO:0000167
4	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	1166764	SO:0001662	SO:0001659	RNA_polymerase_III_TATA_box	SO:0000713
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	1166765	SO:0001662	SO:0000167	RNA_polymerase_III_TATA_box	SO:0001055
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	1166766	SO:0001663	SO:0000713	BREd_motif	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	1166767	SO:0001663	SO:0001203	BREd_motif	SO:0000167
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	1166768	SO:0001664	SO:0000713	DCE	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	1166769	SO:0001664	SO:0001203	DCE	SO:0000167
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	2102387	SO:0001665	SO:0001683	DCE_SI	SO:0001411
4	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	1166771	SO:0001665	SO:0001659	DCE_SI	SO:0000713
4	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	1166772	SO:0001665	SO:0000170	DCE_SI	SO:0001203
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	2102388	SO:0001666	SO:0001683	DCE_SII	SO:0001411
4	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	1166774	SO:0001666	SO:0001659	DCE_SII	SO:0000713
4	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	1166775	SO:0001666	SO:0000170	DCE_SII	SO:0001203
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	2102389	SO:0001667	SO:0001683	DCE_SIII	SO:0001411
4	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	1166777	SO:0001667	SO:0001659	DCE_SIII	SO:0000713
4	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	\N	RNA_polymerase_promoter	\N	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	1166778	SO:0001667	SO:0000170	DCE_SIII	SO:0001203
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	1166779	SO:0001668	SO:0000713	proximal_promoter_element	SO:0000714
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	1166780	SO:0001669	SO:0000167	RNApol_II_core_promoter	SO:0001055
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"" []	SO	1166781	SO:0001670	SO:0000713	distal_promoter_element	SO:0000714
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	2082095	SO:0001671	SO:0001679	bacterial_RNApol_promoter_sigma_70	SO:0005836
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1166783	SO:0001671	SO:0000167	bacterial_RNApol_promoter_sigma_70	SO:0001055
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	2082097	SO:0001672	SO:0001679	bacterial_RNApol_promoter_sigma54	SO:0005836
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1166785	SO:0001672	SO:0000167	bacterial_RNApol_promoter_sigma54	SO:0001055
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	1166786	SO:0001673	SO:0001683	minus_12_signal	SO:0001411
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	1166787	SO:0001673	SO:0000752	minus_12_signal	SO:0001679
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	1166788	SO:0001673	SO:0001203	minus_12_signal	SO:0000167
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	1166789	SO:0001674	SO:0001683	minus_24_signal	SO:0001411
4	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	1166790	SO:0001674	SO:0000752	minus_24_signal	SO:0001679
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	1166791	SO:0001674	SO:0001203	minus_24_signal	SO:0000167
4	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	1166792	SO:0001675	SO:0001659	A_box_type_1	SO:0000713
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	1166793	SO:0001675	SO:0001203	A_box_type_1	SO:0000167
4	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	1166794	SO:0001676	SO:0001659	A_box_type_2	SO:0000713
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	1166795	SO:0001676	SO:0001203	A_box_type_2	SO:0000167
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	1166796	SO:0001677	SO:0000713	intermediate_element	SO:0000714
4	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	1166797	SO:0001677	SO:0001203	intermediate_element	SO:0000167
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	SO	1166798	SO:0001678	SO:0000714	regulatory_promoter_element	SO:0001683
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SO	1166799	SO:0001679	SO:0001411	transcription_regulatory_region	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of translation." [SO:ke]	SO	1166800	SO:0001680	SO:0001411	translation_regulatory_region	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of recombination." [SO:ke]	SO	1166801	SO:0001681	SO:0001411	recombination_regulatory_region	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]	SO	1166802	SO:0001682	SO:0001411	replication_regulatory_region	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]	SO	1166803	SO:0001687	SO:0000001	restriction_enzyme_recognition_site	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	1166804	SO:0001689	SO:0000699	five_prime_restriction_enzyme_junction	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	1166805	SO:0001689	SO:0001954	five_prime_restriction_enzyme_junction	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1166806	SO:0001690	SO:0000699	three_prime_restriction_enzyme_junction	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	1166807	SO:0001690	SO:0001954	three_prime_restriction_enzyme_junction	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166808	SO:0001691	SO:0001411	blunt_end_restriction_enzyme_cleavage_site	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1166809	SO:0001692	SO:0001411	sticky_end_restriction_enzyme_cleavage_site	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	1166810	SO:0001693	SO:0001954	blunt_end_restriction_enzyme_cleavage_junction	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]	SO	1679608	SO:0001695	SO:0000001	restriction_enzyme_single_strand_overhang	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]	SO	1166813	SO:0001697	SO:0000001	ChIP_seq_region	SO:0000110
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	SO	1166814	SO:0001698	SO:0000696	ASPE_primer	SO:0000695
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	SO	1166815	SO:0001699	SO:0000696	dCAPS_primer	SO:0000695
4	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	1166816	SO:0001700	SO:0001067	histone_modification	SO:0100021
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	2712712	SO:0001700	SO:0000001	histone_modification	SO:0000110
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	1166818	SO:0001701	SO:0100001	histone_methylation_site	SO:0001067
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	2885801	SO:0001701	SO:0001411	histone_methylation_site	SO:0000001
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	1166820	SO:0001702	SO:0100001	histone_acetylation_site	SO:0001067
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	2885802	SO:0001702	SO:0001411	histone_acetylation_site	SO:0000001
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166822	SO:0001703	SO:0001700	H3K9_acetylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166823	SO:0001703	SO:0001700	H3K9_acetylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166824	SO:0001704	SO:0001700	H3K14_acetylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166825	SO:0001704	SO:0001700	H3K14_acetylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166826	SO:0001705	SO:0001700	H3K4_monomethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166827	SO:0001705	SO:0001700	H3K4_monomethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166828	SO:0001706	SO:0001700	H3K4_trimethylation	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166829	SO:0001706	SO:0001700	H3K4_trimethylation	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166830	SO:0001707	SO:0001700	H3K9_trimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166831	SO:0001707	SO:0001700	H3K9_trimethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166832	SO:0001708	SO:0001700	H3K27_monomethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166833	SO:0001708	SO:0001700	H3K27_monomethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166834	SO:0001709	SO:0001700	H3K27_trimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166835	SO:0001709	SO:0001700	H3K27_trimethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166836	SO:0001710	SO:0001700	H3K79_monomethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166837	SO:0001710	SO:0001700	H3K79_monomethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166838	SO:0001711	SO:0001700	H3K79_dimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166839	SO:0001711	SO:0001700	H3K79_dimethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166840	SO:0001712	SO:0001700	H3K79_trimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166841	SO:0001712	SO:0001700	H3K79_trimethylation_site	SO:0001720
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166842	SO:0001713	SO:0001089	H4K20_monomethylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166843	SO:0001713	SO:0001720	H4K20_monomethylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166844	SO:0001714	SO:0001089	H2BK5_monomethylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1166845	SO:0001714	SO:0001720	H2BK5_monomethylation_site	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	SO	1166846	SO:0001715	SO:0005836	ISRE	SO:0000831
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	1166847	SO:0001716	SO:0100001	histone_ubiqitination_site	SO:0001067
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	2885827	SO:0001716	SO:0001411	histone_ubiqitination_site	SO:0000001
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	1166849	SO:0001717	SO:0001089	H2B_ubiquitination_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	1166850	SO:0001717	SO:0001720	H2B_ubiquitination_site	SO:0001411
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1166851	SO:0001718	SO:0001700	H3K18_acetylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1166852	SO:0001718	SO:0001700	H3K18_acetylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1166853	SO:0001719	SO:0001700	H3K23_acylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1166854	SO:0001719	SO:0001700	H3K23_acylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1166855	SO:0001721	SO:0001700	H3K27_acylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1166856	SO:0001721	SO:0001700	H3K27_acylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	1166857	SO:0001722	SO:0001700	H3K36_monomethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	1166858	SO:0001722	SO:0001700	H3K36_monomethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	1166859	SO:0001723	SO:0001700	H3K36_dimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	1166860	SO:0001723	SO:0001700	H3K36_dimethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	1166861	SO:0001724	SO:0001700	H3K36_trimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	1166862	SO:0001724	SO:0001700	H3K36_trimethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	1166863	SO:0001725	SO:0001700	H3K4_dimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	1166864	SO:0001725	SO:0001700	H3K4_dimethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	1166865	SO:0001726	SO:0001700	H3K27_dimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	1166866	SO:0001726	SO:0001700	H3K27_dimethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	1166867	SO:0001727	SO:0001700	H3K9_monomethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	1166868	SO:0001727	SO:0001700	H3K9_monomethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	1166869	SO:0001728	SO:0001700	H3K9_dimethylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	1166870	SO:0001728	SO:0001700	H3K9_dimethylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	1166871	SO:0001729	SO:0001700	H4K16_acylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	1166872	SO:0001729	SO:0001700	H4K16_acylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	1166873	SO:0001730	SO:0001700	H4K5_acylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	1166874	SO:0001730	SO:0001700	H4K5_acylation_site	SO:0001720
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	1166875	SO:0001731	SO:0001700	H4K8_acylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	1166876	SO:0001731	SO:0001700	H4K8_acylation_site	SO:0001720
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1166877	SO:0001732	SO:0001089	H3K27_methylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1166878	SO:0001732	SO:0001720	H3K27_methylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1166879	SO:0001733	SO:0001089	H3K36_methylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1166880	SO:0001733	SO:0001720	H3K36_methylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	1166881	SO:0001734	SO:0001089	H3K4_methylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	1166882	SO:0001734	SO:0001720	H3K4_methylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1166883	SO:0001735	SO:0001089	H3K79_methylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1166884	SO:0001735	SO:0001720	H3K79_methylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1166885	SO:0001736	SO:0001089	H3K9_methylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1166886	SO:0001736	SO:0001720	H3K9_methylation_site	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	1166887	SO:0001737	SO:0100001	histone_acylation_region	SO:0001067
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	2885866	SO:0001737	SO:0001411	histone_acylation_region	SO:0000001
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	1166889	SO:0001738	SO:0001089	H4K_acylation_region	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	1166890	SO:0001738	SO:0001720	H4K_acylation_region	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene with a start codon other than AUG." [SO:xp]	SO	1166891	SO:0001739	SO:0000001	gene_with_non_canonical_start_codon	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene with a translational start codon of CUG." [SO:mc]	SO	1166892	SO:0001740	SO:0001411	gene_with_start_codon_CUG	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	SO	1166893	SO:0001741	SO:0000704	pseudogenic_gene_segment	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	SO	1641450	SO:0001741	SO:0001411	pseudogenic_gene_segment	SO:0000001
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166895	SO:0001748	SO:0001420	SL3_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166896	SO:0001749	SO:0001420	SL4_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166897	SO:0001750	SO:0001420	SL5_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166898	SO:0001751	SO:0001420	SL6_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166899	SO:0001752	SO:0001420	SL7_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166900	SO:0001753	SO:0001420	SL8_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166901	SO:0001754	SO:0001420	SL9_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166902	SO:0001755	SO:0001420	SL10_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166903	SO:0001756	SO:0001420	SL11_acceptor_site	SO:0000162
4	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	\N	splice_site	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1166904	SO:0001757	SO:0001420	SL12_acceptor_site	SO:0000162
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]	SO	1166905	SO:0001758	SO:0001411	duplicated_pseudogene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]	SO	1166906	SO:0001759	SO:0001411	unitary_pseudogene	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A pseudogene that arose from a means other than retrotransposition." [SO:ke]	SO	1166907	SO:0001760	SO:0000001	non_processed_pseudogene	SO:0000110
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located within a transcription factor binding site." [EBI:fc]	SO	1166908	SO:0001782	SO:0001537	TF_binding_site_variant	SO:0001060
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	1166909	SO:0001787	SO:0001576	splice_donor_5th_base_variant	SO:0001564
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	2706969	SO:0001788	SO:0000001	U_box	SO:0000110
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	1166911	SO:0001788	SO:0000101	U_box	SO:0001039
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]	SO	1166912	SO:0001789	SO:0000001	mating_type_region	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]	SO	1166913	SO:0001790	SO:0000001	paired_end_fragment	SO:0000110
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that changes exon sequence." [SO:ke]	SO	1166914	SO:0001791	SO:0001878	exon_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	1166915	SO:0001792	SO:0001564	non_coding_transcript_exon_variant	SO:0001878
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	2764391	SO:0001793	SO:0001410	clone_end	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	1166918	SO:0001793	SO:0000148	clone_end	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	1166919	SO:0001793	SO:0000148	clone_end	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	2279476	SO:0001793	SO:0000353	clone_end	SO:0001248
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	1166921	SO:0001793	SO:0001409	clone_end	SO:0000001
4	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	1166922	SO:0001794	SO:0000830	point_centromere	SO:0000340
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	1166923	SO:0001794	SO:0000830	point_centromere	SO:0001411
4	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	1166924	SO:0001795	SO:0000830	regional_centromere	SO:0000340
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	1166925	SO:0001795	SO:0000830	regional_centromere	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	2806657	SO:0001796	SO:0000001	regional_centromere_central_core	SO:0000110
4	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	1166927	SO:0001796	SO:0000628	regional_centromere_central_core	SO:0000830
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A repeat region found within the modular centromere." [SO:ke]	SO	1166928	SO:0001797	SO:0000001	centromeric_repeat	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	2885889	SO:0001798	SO:0001411	regional_centromere_inner_repeat_region	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	1166930	SO:0001798	SO:0001410	regional_centromere_inner_repeat_region	SO:0000001
4	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	1166931	SO:0001798	SO:0000577	regional_centromere_inner_repeat_region	SO:0000628
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	2706972	SO:0001799	SO:0001411	regional_centromere_outer_repeat_region	SO:0000001
4	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	1166933	SO:0001799	SO:0000628	regional_centromere_outer_repeat_region	SO:0000830
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	SO	1166934	SO:0001800	SO:0000673	tasiRNA	SO:0000831
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a tasiRNA." [PMID:16145017]	SO	1166935	SO:0001801	SO:0000673	tasiRNA_primary_transcript	SO:0000831
4	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]	SO	1166936	SO:0001802	SO:0001538	increased_polyadenylation_variant	SO:0001536
4	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]	SO	1166937	SO:0001803	SO:0001538	decreased_polyadenylation_variant	SO:0001536
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	1166938	SO:0001804	SO:0000409	DDB_box	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	1166939	SO:0001804	SO:0100001	DDB_box	SO:0001067
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	1166940	SO:0001805	SO:0100021	destruction_box	SO:0000839
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	SO	1166941	SO:0001806	SO:0000104	ER_retention_signal	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	SO	1641491	SO:0001806	SO:0001411	ER_retention_signal	SO:0000001
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	1166943	SO:0001807	SO:0100021	KEN_box	SO:0000839
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	SO	1166944	SO:0001808	SO:0000104	mitochondrial_targeting_signal	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	SO	1641495	SO:0001808	SO:0001411	mitochondrial_targeting_signal	SO:0000001
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	1166946	SO:0001809	SO:0100011	signal_anchor	SO:0000839
4	"An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]	\N	immature_peptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	1166947	SO:0001809	SO:0100011	signal_anchor	SO:0001063
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	2082232	SO:0001809	SO:0000839	signal_anchor	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	2082233	SO:0001809	SO:0000839	signal_anchor	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	1166950	SO:0001810	SO:0000409	PIP_box	SO:0001411
4	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	1166951	SO:0001810	SO:0100001	PIP_box	SO:0001067
4	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	1166952	SO:0001811	SO:0001067	phosphorylation_site	SO:0100021
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	1641507	SO:0001812	SO:0001070	transmembrane_helix	SO:0000839
4	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	\N	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	1166954	SO:0001812	SO:0001071	transmembrane_helix	SO:0001070
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	SO	1166955	SO:0001813	SO:0000104	vacuolar_sorting_signal	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	SO	1641508	SO:0001813	SO:0001411	vacuolar_sorting_signal	SO:0000001
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]	SO	1166957	SO:0001817	SO:0000733	inframe	SO:0000400
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	1166958	SO:0001818	SO:0001576	protein_altering_variant	SO:0001564
4	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	1166959	SO:0001819	SO:0001576	synonymous_variant	SO:0001564
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	1166960	SO:0001820	SO:0001580	inframe_indel	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	1166961	SO:0001820	SO:0001580	inframe_indel	SO:0001968
4	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	1166962	SO:0001821	SO:0001818	inframe_insertion	SO:0001580
9	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	2885893	SO:0001821	SO:0001878	inframe_insertion	SO:0001537
4	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	1166964	SO:0001822	SO:0001818	inframe_deletion	SO:0001580
10	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	2889312	SO:0001822	SO:0001537	inframe_deletion	SO:0001060
4	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	1166966	SO:0001823	SO:0001650	conservative_inframe_insertion	SO:0001818
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	1166967	SO:0001823	SO:0001907	conservative_inframe_insertion	SO:0001878
4	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	1166968	SO:0001824	SO:0001650	disruptive_inframe_insertion	SO:0001818
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	1166969	SO:0001824	SO:0001907	disruptive_inframe_insertion	SO:0001878
4	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	1166970	SO:0001825	SO:0001650	conservative_inframe_deletion	SO:0001818
10	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	2995464	SO:0001825	SO:0001878	conservative_inframe_deletion	SO:0001537
4	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	1166972	SO:0001826	SO:0001650	disruptive_inframe_deletion	SO:0001818
10	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	2995465	SO:0001826	SO:0001878	disruptive_inframe_deletion	SO:0001537
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	2764395	SO:0001827	SO:0001410	mRNA_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	1166976	SO:0001827	SO:0000148	mRNA_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	1166977	SO:0001827	SO:0000148	mRNA_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	2279480	SO:0001827	SO:0000353	mRNA_read	SO:0001248
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	2764396	SO:0001828	SO:0001410	genomic_DNA_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	1166981	SO:0001828	SO:0000148	genomic_DNA_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	1166982	SO:0001828	SO:0000148	genomic_DNA_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	2279481	SO:0001828	SO:0000353	genomic_DNA_read	SO:0001248
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	2486371	SO:0001829	SO:0001410	mRNA_contig	SO:0000001
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	1166985	SO:0001829	SO:0000719	mRNA_contig	SO:0001876
5	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	1641536	SO:0001829	SO:0001876	mRNA_contig	SO:0000353
7	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	2102390	SO:0001829	SO:0001248	mRNA_contig	SO:0001410
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]	SO	1166988	SO:0001830	SO:0001409	AFLP_fragment	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A match to a protein HMM such as pfam." [SO:ke]	SO	1166989	SO:0001831	SO:0001410	protein_hmm_match	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of immunoglobulin sequence, either constant or variable." [SO:ke]	SO	1259998	SO:0001832	SO:0000001	immunoglobulin_region	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	1166992	SO:0001833	SO:0000104	V_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	1641541	SO:0001833	SO:0001411	V_region	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	1166994	SO:0001834	SO:0000104	C_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	1641543	SO:0001834	SO:0001411	C_region	SO:0000001
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	1166996	SO:0001835	SO:0000299	N_region	SO:0000669
4	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	1166997	SO:0001836	SO:0000299	S_region	SO:0000669
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]	SO	1166998	SO:0001837	SO:0000001	mobile_element_insertion	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]	SO	1166999	SO:0001838	SO:0000001	novel_sequence_insertion	SO:0000110
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	SO	1167000	SO:0001839	SO:0000714	CSL_response_element	SO:0001683
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	1167001	SO:0001840	SO:0000713	GATA_box	SO:0000714
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]	SO	1167002	SO:0001841	SO:0000001	polymorphic_pseudogene	SO:0000110
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	SO	1167003	SO:0001842	SO:0000714	AP_1_binding_site	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	SO	1167004	SO:0001843	SO:0000714	CRE	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	SO	1167005	SO:0001844	SO:0000714	CuRE	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	SO	1167006	SO:0001845	SO:0000714	DRE	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	SO	1167007	SO:0001846	SO:0000714	FLEX_element	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	SO	1167008	SO:0001847	SO:0000714	forkhead_motif	SO:0001683
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	1167009	SO:0001848	SO:0000713	homol_D_box	SO:0000714
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	SO	1167010	SO:0001849	SO:0000714	homol_E_box	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	SO	1167011	SO:0001850	SO:0000714	HSE	SO:0001683
4	"A motif that is active in the DNA form of the sequence." [SO:ke]	\N	DNA_motif	\N	\N	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	1167012	SO:0001851	SO:0001659	iron_repressed_GATA_element	SO:0000713
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	SO	1167013	SO:0001852	SO:0000714	mating_type_M_box	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]	SO	1167014	SO:0001853	SO:0001683	androgen_response_element	SO:0001411
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]	SO	1167015	SO:0001854	SO:0000695	smFISH_probe	SO:0001409
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	SO	1167016	SO:0001855	SO:0000714	MCB	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	SO	1167017	SO:0001856	SO:0000714	CCAAT_motif	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	SO	1167018	SO:0001857	SO:0000714	Ace2_UAS	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	SO	1167019	SO:0001858	SO:0000714	TR_box	SO:0001683
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	SO	1167020	SO:0001859	SO:0000714	STREP_motif	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]	SO	1167021	SO:0001860	SO:0001683	rDNA_intergenic_spacer_element	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	SO	1167022	SO:0001861	SO:0000714	sterol_regulatory_element	SO:0001683
4	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	\N	tandem_repeat	SOFA	SOFA	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	1167023	SO:0001862	SO:0000005	GT_dinucleotide_repeat	SO:0000705
4	"Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]	\N	tandem_repeat	SOFA	SOFA	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	1167024	SO:0001863	SO:0000005	GTT_trinucleotide_repeat	SO:0000705
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]	SO	1167025	SO:0001864	SO:0001683	Sap1_recognition_motif	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	SO	1167026	SO:0001865	SO:0000714	CDRE_motif	SO:0001683
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	2486373	SO:0001866	SO:0001410	BAC_read_contig	SO:0000001
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	1167028	SO:0001866	SO:0000719	BAC_read_contig	SO:0001876
5	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A contig of BAC reads." [GMOD:ea]	SO	1641574	SO:0001866	SO:0001876	BAC_read_contig	SO:0000353
7	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	2102391	SO:0001866	SO:0001248	BAC_read_contig	SO:0001410
4	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	1167031	SO:0001866	SO:0000151	BAC_read_contig	SO:0000695
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	1167032	SO:0001866	SO:0001235	BAC_read_contig	SO:0001411
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene suspected of being involved in the expression of a trait." [GMOD:ea]	SO	1167033	SO:0001867	SO:0000001	candidate_gene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]	SO	1167034	SO:0001868	SO:0001411	positional_candidate_gene	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]	SO	1167035	SO:0001869	SO:0001411	functional_candidate_gene	SO:0000001
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	SO	1167036	SO:0001870	SO:0000673	enhancerRNA	SO:0000831
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	SO	1167037	SO:0001871	SO:0000714	PCB	SO:0001683
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	SO	1167038	SO:0001873	SO:0000001	interchromosomal_breakpoint	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A rearrangement breakpoint between two different chromosomes." [NCBI:th]	SO	1167039	SO:0001873	SO:0001059	interchromosomal_breakpoint	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	SO	1167040	SO:0001874	SO:0000001	intrachromosomal_breakpoint	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A rearrangement breakpoint within the same chromosome." [NCBI:th]	SO	1167041	SO:0001874	SO:0001059	intrachromosomal_breakpoint	SO:0000110
5	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	1259999	SO:0001875	SO:0000353	unassigned_supercontig	SO:0001248
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SO	1167044	SO:0001876	SO:0001410	partial_genomic_sequence_assembly	SO:0000001
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	SO	1167045	SO:0001877	SO:0000673	lnc_RNA	SO:0000831
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature translocation where the region contains a transcription factor binding site." [SO:ke]	SO	1167046	SO:0001885	SO:0001537	TFBS_translocation	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A fusion where the deletion brings together transcription factor binding sites." [SO:ke]	SO	1167047	SO:0001888	SO:0001537	TFBS_fusion	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature amplification of a region containing a transcription factor binding site." [SO:ke]	SO	1167048	SO:0001892	SO:0001537	TFBS_amplification	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]	SO	1167049	SO:0001895	SO:0001537	TFBS_ablation	SO:0001060
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	1167050	SO:0001896	SO:0000234	transposable_element_CDS	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	1167051	SO:0001896	SO:0000834	transposable_element_CDS	SO:0000833
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	1167052	SO:0001896	SO:0001037	transposable_element_CDS	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	1167053	SO:0001896	SO:0001037	transposable_element_CDS	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	1679611	SO:0001897	SO:0000001	transposable_element_pseudogene	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	1167055	SO:0001897	SO:0001037	transposable_element_pseudogene	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A pseudogene contained within a transposable element." [SO:ke]	SO	1167056	SO:0001897	SO:0001037	transposable_element_pseudogene	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2885900	SO:0001898	SO:0001411	dg_repeat	SO:0000001
4	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	1167058	SO:0001898	SO:0000577	dg_repeat	SO:0000628
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2885901	SO:0001899	SO:0001411	dh_repeat	SO:0000001
4	"" []	\N	chromosomal_structural_element	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	1167060	SO:0001899	SO:0000577	dh_repeat	SO:0000628
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]	SO	1167061	SO:0001900	SO:0001683	M26_binding_site	SO:0001411
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	1167062	SO:0001901	SO:0000713	AACCCT_box	SO:0000714
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	1805765	SO:0001902	SO:0001411	splice_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	1260002	SO:0001902	SO:0000831	splice_region	SO:0001411
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	1167065	SO:0001903	SO:0000233	intronic_lncRNA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	1167066	SO:0001904	SO:0000233	antisense_lncRNA	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]	SO	1167067	SO:0001905	SO:0000831	regional_centromere_outer_repeat_transcript	SO:0001411
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]	SO	1167068	SO:0001908	SO:0001537	internal_feature_elongation	SO:0001060
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	1167069	SO:0001909	SO:0001580	frameshift_elongation	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	1167070	SO:0001909	SO:0001580	frameshift_elongation	SO:0001968
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	2706999	SO:0001909	SO:0001878	frameshift_elongation	SO:0001537
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	1167072	SO:0001910	SO:0001580	frameshift_truncation	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	1167073	SO:0001910	SO:0001580	frameshift_truncation	SO:0001968
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	2712713	SO:0001910	SO:0001537	frameshift_truncation	SO:0001060
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	2082312	SO:0001913	SO:0001679	bacterial_RNApol_promoter_sigma_ecf	SO:0005836
4	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	1167076	SO:0001913	SO:0000167	bacterial_RNApol_promoter_sigma_ecf	SO:0001055
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]	SO	1167077	SO:0001914	SO:0001683	rDNA_replication_fork_barrier	SO:0001411
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]	SO	1167078	SO:0001916	SO:0000695	CAGE_tag	SO:0001409
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]	SO	1167079	SO:0001917	SO:0000001	CAGE_cluster	SO:0000110
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	1167080	SO:0001918	SO:0000305	5_methylcytosine	SO:0001236
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	1167081	SO:0001918	SO:0000305	5_methylcytosine	SO:0001720
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	1167082	SO:0001919	SO:0000305	4_methylcytosine	SO:0001236
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	1167083	SO:0001919	SO:0000305	4_methylcytosine	SO:0001720
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	1167084	SO:0001920	SO:0000305	N6_methyladenine	SO:0001236
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	1167085	SO:0001920	SO:0000305	N6_methyladenine	SO:0001720
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	2486377	SO:0001921	SO:0001410	mitochondrial_contig	SO:0000001
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	1167087	SO:0001921	SO:0000719	mitochondrial_contig	SO:0001876
5	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	1641620	SO:0001921	SO:0001876	mitochondrial_contig	SO:0000353
7	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	2102392	SO:0001921	SO:0001248	mitochondrial_contig	SO:0001410
5	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	1260003	SO:0001922	SO:0000353	mitochondrial_supercontig	SO:0001248
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	1167092	SO:0001923	SO:0000233	TERRA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	1167093	SO:0001924	SO:0000233	ARRET	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	1167094	SO:0001925	SO:0000233	ARIA	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	1167095	SO:0001926	SO:0000233	anti_ARRET	SO:0000673
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	SO	1167096	SO:0001927	SO:0000673	telomeric_transcript	SO:0000831
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A duplication of the distal region of a chromosome." [SO:bm]	SO	1167097	SO:0001928	SO:0001059	distal_duplication	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A duplication of the distal region of a chromosome." [SO:bm]	SO	1167098	SO:0001928	SO:0001411	distal_duplication	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	2764398	SO:0001929	SO:0001410	mitochondrial_DNA_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	1167101	SO:0001929	SO:0000148	mitochondrial_DNA_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	1167102	SO:0001929	SO:0000148	mitochondrial_DNA_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	2279485	SO:0001929	SO:0000353	mitochondrial_DNA_read	SO:0001248
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	2764399	SO:0001930	SO:0001410	chloroplast_DNA_read	SO:0000001
4	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	\N	ultracontig	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	1167106	SO:0001930	SO:0000148	chloroplast_DNA_read	SO:0000719
4	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	1167107	SO:0001930	SO:0000148	chloroplast_DNA_read	SO:0001876
7	"A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]	\N	assembly	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	2279486	SO:0001930	SO:0000353	chloroplast_DNA_read	SO:0001248
4	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	1167110	SO:0001932	SO:0001687	restriction_enzyme_five_prime_single_strand_overhang	SO:0001954
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	1679613	SO:0001932	SO:0001411	restriction_enzyme_five_prime_single_strand_overhang	SO:0000001
4	"A region related to restriction enzyme function." [SO:ke]	\N	restriction_enzyme_region	\N	\N	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	1167112	SO:0001933	SO:0001687	restriction_enzyme_three_prime_single_strand_overhang	SO:0001954
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	1679614	SO:0001933	SO:0001411	restriction_enzyme_three_prime_single_strand_overhang	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]	SO	1167114	SO:0001934	SO:0001411	monomeric_repeat	SO:0000001
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	1167115	SO:0001935	SO:0001089	H3K20_trimethylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	1167116	SO:0001935	SO:0001720	H3K20_trimethylation_site	SO:0001411
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	1167117	SO:0001936	SO:0001700	H3K36_acetylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	1167118	SO:0001936	SO:0001700	H3K36_acetylation_site	SO:0001720
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	1167119	SO:0001937	SO:0001089	H2BK12_acetylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	1167120	SO:0001937	SO:0001720	H2BK12_acetylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	1167121	SO:0001938	SO:0001089	H2AK5_acetylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	1167122	SO:0001938	SO:0001720	H2AK5_acetylation_site	SO:0001411
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	1167123	SO:0001939	SO:0001700	H4K12_acetylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	1167124	SO:0001939	SO:0001700	H4K12_acetylation_site	SO:0001720
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1167125	SO:0001940	SO:0001089	H2BK120_acetylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1167126	SO:0001940	SO:0001720	H2BK120_acetylation_site	SO:0001411
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	1167127	SO:0001941	SO:0001700	H4K91_acetylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	1167128	SO:0001941	SO:0001700	H4K91_acetylation_site	SO:0001720
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1167129	SO:0001942	SO:0001089	H2BK20_acetylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1167130	SO:0001942	SO:0001720	H2BK20_acetylation_site	SO:0001411
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	1167131	SO:0001943	SO:0001700	H3K4ac_acetylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	1167132	SO:0001943	SO:0001700	H3K4ac_acetylation_site	SO:0001720
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	1167133	SO:0001944	SO:0001089	H2AK9_acetylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	1167134	SO:0001944	SO:0001720	H2AK9_acetylation_site	SO:0001411
4	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	\N	post_translationally_modified_region	biosapiens	\N	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	1167135	SO:0001945	SO:0001700	H3K56_acetylation_site	SO:0001089
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	\N	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	1167136	SO:0001945	SO:0001700	H3K56_acetylation_site	SO:0001720
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1167137	SO:0001946	SO:0001089	H2BK15_acetylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1167138	SO:0001946	SO:0001720	H2BK15_acetylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	1167139	SO:0001947	SO:0001089	H3R2_monomethylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	1167140	SO:0001947	SO:0001720	H3R2_monomethylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	1167141	SO:0001948	SO:0001089	H3R2_dimethylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	1167142	SO:0001948	SO:0001720	H3R2_dimethylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	1167143	SO:0001949	SO:0001089	H4R3_dimethylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	1167144	SO:0001949	SO:0001720	H4R3_dimethylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	1167145	SO:0001950	SO:0001089	H4K4_trimethylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	1167146	SO:0001950	SO:0001720	H4K4_trimethylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	1167147	SO:0001951	SO:0001089	H3K23_dimethylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	1167148	SO:0001951	SO:0001720	H3K23_dimethylation_site	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	SO	1167149	SO:0001952	SO:0005836	promoter_flanking_region	SO:0000831
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]	SO	1167150	SO:0001953	SO:0000001	restriction_enzyme_assembly_scar	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]	SO	1260006	SO:0001955	SO:0000001	protein_stability_element	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide_region that  codes for a protease cleavage site." [SO:ke]	SO	1260007	SO:0001956	SO:0000001	protease_site	SO:0000110
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	1167155	SO:0001958	SO:0000185	lariat_intron	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	1167156	SO:0001958	SO:0000833	lariat_intron	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	1167157	SO:0001958	SO:0000833	lariat_intron	SO:0001411
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	1167158	SO:0001959	SO:0000713	TCT_motif	SO:0000714
4	"A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]	\N	base	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	1167159	SO:0001960	SO:0000305	5_hydroxymethylcytosine	SO:0001236
4	"A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	\N	epigenetically_modified_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	1167160	SO:0001960	SO:0000305	5_hydroxymethylcytosine	SO:0001720
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	1167161	SO:0001961	SO:0001236	5_formylcytosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	1167162	SO:0001961	SO:0001720	5_formylcytosine	SO:0001411
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified adenine DNA base feature." [SO:ke]	SO	1167163	SO:0001962	SO:0001411	modified_adenine	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified cytosine DNA base feature." [SO:ke]	SO	1167164	SO:0001963	SO:0001411	modified_cytosine	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified guanine DNA base feature." [SO:ke]	SO	1167165	SO:0001964	SO:0001411	modified_guanine	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	1167166	SO:0001965	SO:0001236	8_oxoguanine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	1167167	SO:0001965	SO:0001720	8_oxoguanine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	1167168	SO:0001966	SO:0001236	5_carboxylcytosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	1167169	SO:0001966	SO:0001720	5_carboxylcytosine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	1167170	SO:0001967	SO:0001236	8_oxoadenine	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	1167171	SO:0001967	SO:0001720	8_oxoadenine	SO:0001411
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant of a protein coding gene." [SO:ke]	SO	1167172	SO:0001968	SO:0001878	coding_transcript_variant	SO:0001537
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	1167173	SO:0001969	SO:0001564	coding_transcript_intron_variant	SO:0001878
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	1167174	SO:0001970	SO:0001564	non_coding_transcript_intron_variant	SO:0001878
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"" []	SO	1167175	SO:0001971	SO:0000409	zinc_finger_binding_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	1167176	SO:0001972	SO:0001089	histone_4_acylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	1167177	SO:0001972	SO:0001720	histone_4_acylation_site	SO:0001411
4	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	1167178	SO:0001973	SO:0001089	histone_3_acetylation_site	SO:0100001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	1167179	SO:0001973	SO:0001720	histone_3_acetylation_site	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	SO	1167180	SO:0001974	SO:0000714	CTCF_binding_site	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]	SO	1167181	SO:0001975	SO:0001954	five_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]	SO	1167182	SO:0001976	SO:0001954	three_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	SO	1167183	SO:0001977	SO:0000831	ribonuclease_site	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]	SO	1679615	SO:0001977	SO:0000001	ribonuclease_site	SO:0000110
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A motif that affects the stability of RNA." [PMID:22495308, SO:ke]	SO	1167186	SO:0001979	SO:0001683	RNA_stability_element	SO:0001411
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	1167187	SO:0001980	SO:0000713	G_box	SO:0000714
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	1167188	SO:0001981	SO:0000713	L_box	SO:0000714
4	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	1167189	SO:0001982	SO:0000713	I-box	SO:0000714
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	1167190	SO:0001983	SO:0001791	5_prime_UTR_premature_start_codon_variant	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	1167191	SO:0001983	SO:0001968	5_prime_UTR_premature_start_codon_variant	SO:0001576
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]	SO	1167192	SO:0001984	SO:0001411	silent_mating_type_cassette_array	SO:0000001
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]	SO	1167193	SO:0001986	SO:0001537	upstream_transcript_variant	SO:0001060
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"" []	SO	1167194	SO:0001987	SO:0001537	downstream_transcript_variant	SO:0001060
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	1167195	SO:0001988	SO:0001622	5_prime_UTR_premature_start_codon_gain_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	1167196	SO:0001988	SO:0001622	5_prime_UTR_premature_start_codon_gain_variant	SO:0001968
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	1167197	SO:0001989	SO:0001622	5_prime_UTR_premature_start_codon_loss_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	1167198	SO:0001989	SO:0001622	5_prime_UTR_premature_start_codon_loss_variant	SO:0001968
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	1167199	SO:0001990	SO:0001622	five_prime_UTR_premature_start_codon_location_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	1167200	SO:0001990	SO:0001622	five_prime_UTR_premature_start_codon_location_variant	SO:0001968
4	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	1167202	SO:0001992	SO:0001580	nonsynonymous_variant	SO:0001791
4	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	1167203	SO:0001992	SO:0001580	nonsynonymous_variant	SO:0001968
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	1167204	SO:0001993	SO:0000835	extended_cis_splice_site	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	1167205	SO:0001993	SO:0000835	extended_cis_splice_site	SO:0000833
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	1679616	SO:0001994	SO:0000185	intron_base_5	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	1679617	SO:0001994	SO:0000833	intron_base_5	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	1679618	SO:0001994	SO:0000833	intron_base_5	SO:0001411
4	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	1167211	SO:0001994	SO:0000162	intron_base_5	SO:0000835
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]	SO	1167212	SO:0001995	SO:0001564	extended_intronic_splice_region_variant	SO:0001878
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	1260011	SO:0001996	SO:0000185	extended_intronic_splice_region	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	1260012	SO:0001996	SO:0000833	extended_intronic_splice_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	1260013	SO:0001996	SO:0000833	extended_intronic_splice_region	SO:0001411
4	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	1167218	SO:0001997	SO:0000340	subtelomere	SO:0001235
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	2082399	SO:0001997	SO:0001411	subtelomere	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]	SO	1167220	SO:0001998	SO:0001409	sgRNA	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	1167221	SO:0001999	SO:0001683	mating_type_region_motif	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	1641729	SO:0001999	SO:0001411	mating_type_region_motif	SO:0000001
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	1167223	SO:0002000	SO:0000714	W_region	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	1167224	SO:0002000	SO:0005855	W_region	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	1167225	SO:0002001	SO:0000714	Y_region	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	1167226	SO:0002001	SO:0005855	Y_region	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1167227	SO:0002002	SO:0000714	Z1_region	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1167228	SO:0002002	SO:0005855	Z1_region	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	1167229	SO:0002003	SO:0000714	Z2_region	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	1167230	SO:0002003	SO:0005855	Z2_region	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	1167231	SO:0002004	SO:0001683	ARS_consensus_sequence	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	1167232	SO:0002004	SO:0001235	ARS_consensus_sequence	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	1641739	SO:0002004	SO:0001411	ARS_consensus_sequence	SO:0000001
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]	SO	1167234	SO:0002005	SO:0001683	DSR_motif	SO:0001411
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	SO	1167235	SO:0002006	SO:0000714	zinc_repressed_element	SO:0001683
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]	SO	1167236	SO:0002007	SO:0000001	MNV	SO:0000110
4	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	1167237	SO:0002008	SO:0001992	rare_amino_acid_variant	SO:0001650
4	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	1167238	SO:0002009	SO:0001583	selenocysteine_loss	SO:0001992
4	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	\N	nonsynonymous_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	1167239	SO:0002010	SO:0001583	pyrrolysine_loss	SO:0001992
4	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence." [SO:ke]	SO	1167240	SO:0002011	SO:0001878	intragenic_variant	SO:0001537
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	1679619	SO:0002012	SO:0001791	start_lost	SO:0001576
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	1679620	SO:0002012	SO:0001968	start_lost	SO:0001576
4	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	1167243	SO:0002012	SO:0001818	start_lost	SO:0001580
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	1167244	SO:0002013	SO:0001791	5_prime_UTR_truncation	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	1167245	SO:0002013	SO:0001968	5_prime_UTR_truncation	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	1167246	SO:0002014	SO:0001791	5_prime_UTR_elongation	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	1167247	SO:0002014	SO:0001968	5_prime_UTR_elongation	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	1167248	SO:0002015	SO:0001791	3_prime_UTR_truncation	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	1167249	SO:0002015	SO:0001968	3_prime_UTR_truncation	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	1167250	SO:0002016	SO:0001791	3_prime_UTR_elongation	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	1167251	SO:0002016	SO:0001968	3_prime_UTR_elongation	SO:0001576
4	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located in a conserved intergenic region, between genes." [SO:ke]	SO	1167252	SO:0002017	SO:0001537	conserved_intergenic_variant	SO:0001060
4	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A transcript variant occurring within a conserved region of an intron." [SO:ke]	SO	1167253	SO:0002018	SO:0001564	conserved_intron_variant	SO:0001878
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	1167254	SO:0002019	SO:0001791	start_retained_variant	SO:0001576
4	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	1167255	SO:0002019	SO:0001968	start_retained_variant	SO:0001576
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]	SO	1167256	SO:0002020	SO:0001683	boundary_element	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]	SO	1167257	SO:0002021	SO:0001683	mating_type_region_replication_fork_barrier	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	SO	1167258	SO:0002022	SO:0000673	priRNA	SO:0000831
4	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]	SO	1167259	SO:0002023	SO:0000695	multiplexing_sequence_identifier	SO:0001409
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1167260	SO:0002024	SO:0000714	W_region	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1167261	SO:0002024	SO:0005855	W_region	SO:0001411
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	SO	1167262	SO:0002025	SO:0001683	cis_acting_homologous_chromosome_pairing_region	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]	SO	1260014	SO:0002026	SO:0000001	intein_encoding_region	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]	SO	1167265	SO:0002027	SO:0001410	uORF	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]	SO	1167266	SO:0002028	SO:0001410	sORF	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]	SO	1167267	SO:0002029	SO:0001410	tnaORF	SO:0000001
4	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1167268	SO:0002030	SO:0000714	X_region	SO:0001683
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1167269	SO:0002030	SO:0005855	X_region	SO:0001411
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	SO	1167270	SO:0002031	SO:0000673	shRNA	SO:0000831
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of sequence that is involved in the control of a biological process." [SO:ke]	SO	1167271	SO:0005836	SO:0000001	regulatory_region	SO:0000110
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	1167272	SO:0005837	SO:0000185	U14_snoRNA_primary_transcript	SO:0000673
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	1167273	SO:0005841	SO:0000655	methylation_guide_snoRNA	SO:0000233
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	SO	1167274	SO:0005843	SO:0000673	rRNA_cleavage_RNA	SO:0000831
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	1167275	SO:0005845	SO:0000673	exon_of_single_exon_gene	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	2082433	SO:0005845	SO:0001411	exon_of_single_exon_gene	SO:0000001
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"" []	SO	1167277	SO:0005847	SO:0000401	cassette_array_member	SO:0000733
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1167278	SO:0005848	SO:0000733	gene_cassette_member	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1167279	SO:0005849	SO:0000733	gene_subarray_member	SO:0000400
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441990	SO:0005850	SO:0001411	primer_binding_site	SO:0000001
4	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1167281	SO:0005850	SO:0000101	primer_binding_site	SO:0001039
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]	SO	1167282	SO:0005851	SO:0000001	gene_array	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]	SO	1167283	SO:0005852	SO:0000001	gene_subarray	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]	SO	1167284	SO:0005853	SO:0000001	gene_cassette	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]	SO	1167285	SO:0005854	SO:0000001	gene_cassette_array	SO:0000110
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	1167286	SO:0005856	SO:0000185	selenocysteine_tRNA_primary_transcript	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	1167287	SO:0005857	SO:0000233	selenocysteinyl_tRNA	SO:0000673
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]	SO	1167288	SO:0005858	SO:0000001	syntenic_region	SO:0000110
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	1167289	SO:0100001	SO:0000839	biochemical_region_of_peptide	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	1167290	SO:0100001	SO:0000839	biochemical_region_of_peptide	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	1167291	SO:0100002	SO:0100021	molecular_contact_region	SO:0000839
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	SO	1167292	SO:0100003	SO:0000104	intrinsically_unstructured_polypeptide_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	SO	1641783	SO:0100003	SO:0001411	intrinsically_unstructured_polypeptide_region	SO:0000001
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167294	SO:0100004	SO:0000839	catmat_left_handed_three	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167295	SO:0100004	SO:0000839	catmat_left_handed_three	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167296	SO:0100005	SO:0000839	catmat_left_handed_four	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167297	SO:0100005	SO:0000839	catmat_left_handed_four	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167298	SO:0100006	SO:0000839	catmat_right_handed_three	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167299	SO:0100006	SO:0000839	catmat_right_handed_three	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167300	SO:0100007	SO:0000839	catmat_right_handed_four	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167301	SO:0100007	SO:0000839	catmat_right_handed_four	SO:0001411
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167302	SO:0100008	SO:0000839	alpha_beta_motif	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1167303	SO:0100008	SO:0000839	alpha_beta_motif	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	1260015	SO:0100009	SO:0000104	lipoprotein_signal_peptide	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	1805778	SO:0100009	SO:0001411	lipoprotein_signal_peptide	SO:0000001
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]	SO	1167308	SO:0100010	SO:0001410	no_output	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens,SOFA	sequence_feature	SOFA	SOFA	sequence	"The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]	SO	1679621	SO:0100011	SO:0000001	cleaved_peptide_region	SO:0000110
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	1167310	SO:0100012	SO:0000839	peptide_coil	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	1167311	SO:0100012	SO:0000839	peptide_coil	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]	SO	1260019	SO:0100013	SO:0000001	hydrophobic_region_of_peptide	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	2102393	SO:0100014	SO:0000104	n_terminal_region	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	2486381	SO:0100014	SO:0001411	n_terminal_region	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	2102395	SO:0100015	SO:0000104	c_terminal_region	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	2486383	SO:0100015	SO:0001411	c_terminal_region	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	2102397	SO:0100016	SO:0000104	central_hydrophobic_region_of_signal_peptide	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	2486385	SO:0100016	SO:0001411	central_hydrophobic_region_of_signal_peptide	SO:0000001
4	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	1167332	SO:0100017	SO:0000839	polypeptide_conserved_motif	SO:0000104
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	1167333	SO:0100017	SO:0000839	polypeptide_conserved_motif	SO:0001411
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	1167334	SO:0100018	SO:0100021	polypeptide_binding_motif	SO:0000839
4	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	1167335	SO:0100019	SO:0100021	polypeptide_catalytic_motif	SO:0000839
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	1167336	SO:0100020	SO:0000409	polypeptide_DNA_contact	SO:0001411
4	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	1167337	SO:0100020	SO:0001067	polypeptide_DNA_contact	SO:0100021
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	1260026	SO:0100021	SO:0000001	polypeptide_conserved_region	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1167340	SO:1000005	SO:0000001	complex_substitution	SO:0000110
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SO	1167341	SO:1000008	SO:0001059	point_mutation	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SO	1167342	SO:1000008	SO:0001411	point_mutation	SO:0000001
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1167343	SO:1000009	SO:0001059	transition	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1167344	SO:1000009	SO:0001411	transition	SO:0000001
4	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	1167345	SO:1000010	SO:1000002	pyrimidine_transition	SO:0001059
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	1167346	SO:1000010	SO:1000002	pyrimidine_transition	SO:0001411
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	1167347	SO:1000011	SO:0001483	C_to_T_transition	SO:1000002
4	"SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]	\N	SNV	SOFA	\N	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1167348	SO:1000012	SO:1000009	C_to_T_transition_at_pCpG_site	SO:0001483
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"" []	SO	1167349	SO:1000013	SO:0001483	T_to_C_transition	SO:1000002
4	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	1167350	SO:1000014	SO:1000002	purine_transition	SO:0001059
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	1167351	SO:1000014	SO:1000002	purine_transition	SO:0001411
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	1167352	SO:1000015	SO:0001483	A_to_G_transition	SO:1000002
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	1167353	SO:1000016	SO:0001483	G_to_A_transition	SO:1000002
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1167354	SO:1000017	SO:0001059	transversion	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1167355	SO:1000017	SO:0001411	transversion	SO:0000001
4	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	1167356	SO:1000018	SO:1000002	pyrimidine_to_purine_transversion	SO:0001059
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	1167357	SO:1000018	SO:1000002	pyrimidine_to_purine_transversion	SO:0001411
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	1167358	SO:1000019	SO:0001483	C_to_A_transversion	SO:1000002
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"" []	SO	1167359	SO:1000020	SO:0001483	C_to_G_transversion	SO:1000002
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transversion from T to A." [SO:ke]	SO	1167360	SO:1000021	SO:0001483	T_to_A_transversion	SO:1000002
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transversion from T to G." [SO:ke]	SO	1167361	SO:1000022	SO:0001483	T_to_G_transversion	SO:1000002
4	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	1167362	SO:1000023	SO:1000002	purine_to_pyrimidine_transversion	SO:0001059
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	1167363	SO:1000023	SO:1000002	purine_to_pyrimidine_transversion	SO:0001411
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	1167364	SO:1000024	SO:0001483	A_to_C_transversion	SO:1000002
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	1167365	SO:1000025	SO:0001483	A_to_T_transversion	SO:1000002
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	1167366	SO:1000026	SO:0001483	G_to_C_transversion	SO:1000002
4	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	1167367	SO:1000027	SO:0001483	G_to_T_transversion	SO:1000002
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	1167368	SO:1000028	SO:0001507	intrachromosomal_mutation	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	1167369	SO:1000028	SO:0001524	intrachromosomal_mutation	SO:0001506
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	1167370	SO:1000029	SO:0000240	chromosomal_deletion	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	1167371	SO:1000029	SO:0000240	chromosomal_deletion	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	1167372	SO:1000030	SO:0000240	chromosomal_inversion	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	1167373	SO:1000030	SO:0000240	chromosomal_inversion	SO:0001524
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	1167374	SO:1000031	SO:0001507	interchromosomal_mutation	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	1167375	SO:1000031	SO:0001524	interchromosomal_mutation	SO:0001506
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	SO	1167376	SO:1000035	SO:0000001	duplication	SO:0000110
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	1167377	SO:1000037	SO:0001507	chromosomal_duplication	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	1167378	SO:1000037	SO:0001524	chromosomal_duplication	SO:0001506
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	1167379	SO:1000038	SO:0000240	intrachromosomal_duplication	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	1167380	SO:1000038	SO:0000240	intrachromosomal_duplication	SO:0001524
4	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	1167381	SO:1000039	SO:0000667	direct_tandem_duplication	SO:0001059
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	DBVAR,SOFA	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	1167382	SO:1000039	SO:0000667	direct_tandem_duplication	SO:0001411
4	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	DBVAR,SOFA	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	1167383	SO:1000040	SO:0000667	inverted_tandem_duplication	SO:0001059
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	DBVAR,SOFA	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	1167384	SO:1000040	SO:0000667	inverted_tandem_duplication	SO:0001411
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	1260027	SO:1000041	SO:0000240	intrachromosomal_transposition	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	1260028	SO:1000041	SO:0000240	intrachromosomal_transposition	SO:0001524
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	1167387	SO:1000042	SO:0001507	compound_chromosome	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	1167388	SO:1000042	SO:0001524	compound_chromosome	SO:0001506
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	1167389	SO:1000043	SO:1000183	Robertsonian_fusion	SO:0000240
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	1167390	SO:1000044	SO:0000240	chromosomal_translocation	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	1167391	SO:1000044	SO:0000240	chromosomal_translocation	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	1167392	SO:1000045	SO:0000240	ring_chromosome	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	1167393	SO:1000045	SO:0000240	ring_chromosome	SO:0001524
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	1167394	SO:1000046	SO:1000183	pericentric_inversion	SO:0000240
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	1167395	SO:1000047	SO:1000183	paracentric_inversion	SO:0000240
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	1167396	SO:1000048	SO:1000183	reciprocal_chromosomal_translocation	SO:0000240
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	1167397	SO:1000136	SO:0001507	autosynaptic_chromosome	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	1167398	SO:1000136	SO:0001524	autosynaptic_chromosome	SO:0001506
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	1167399	SO:1000138	SO:0000240	homo_compound_chromosome	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	1167400	SO:1000138	SO:0000240	homo_compound_chromosome	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	1167401	SO:1000140	SO:0000240	hetero_compound_chromosome	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	1167402	SO:1000140	SO:0000240	hetero_compound_chromosome	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	1167403	SO:1000141	SO:0000240	chromosome_fission	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	1167404	SO:1000141	SO:0000240	chromosome_fission	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	1167405	SO:1000142	SO:0000240	dexstrosynaptic_chromosome	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	1167406	SO:1000142	SO:0000240	dexstrosynaptic_chromosome	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	1167407	SO:1000143	SO:0000240	laevosynaptic_chromosome	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	1167408	SO:1000143	SO:0000240	laevosynaptic_chromosome	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	1167409	SO:1000144	SO:0000240	free_duplication	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	1167410	SO:1000144	SO:0000240	free_duplication	SO:0001524
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	1167411	SO:1000145	SO:1000183	free_ring_duplication	SO:0000240
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	1167412	SO:1000146	SO:0001507	complex_chromosomal_mutation	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	1167413	SO:1000146	SO:0001524	complex_chromosomal_mutation	SO:0001506
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	1167414	SO:1000147	SO:1000183	deficient_translocation	SO:0000240
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	1260029	SO:1000148	SO:0000240	inversion_cum_translocation	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	1260030	SO:1000148	SO:0000240	inversion_cum_translocation	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	1260031	SO:1000149	SO:0000240	bipartite_duplication	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	1260032	SO:1000149	SO:0000240	bipartite_duplication	SO:0001524
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	1167420	SO:1000150	SO:1000183	cyclic_translocation	SO:0000240
4	"" []	\N	chromosome_variation	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	1167421	SO:1000151	SO:1000183	bipartite_inversion	SO:0000240
4	"" []	\N	chromosome_variation	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1167422	SO:1000152	SO:1000183	uninverted_insertional_duplication	SO:0000240
4	"" []	\N	chromosome_variation	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1167423	SO:1000153	SO:1000183	inverted_insertional_duplication	SO:0000240
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	1167424	SO:1000154	SO:0000240	insertional_duplication	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	1167425	SO:1000154	SO:0000240	insertional_duplication	SO:0001524
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	1167426	SO:1000155	SO:0000240	interchromosomal_transposition	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	1167427	SO:1000155	SO:0000240	interchromosomal_transposition	SO:0001524
4	"" []	\N	chromosome_variation	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	1167428	SO:1000156	SO:1000183	inverted_interchromosomal_transposition	SO:0000240
4	"" []	\N	chromosome_variation	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1167429	SO:1000157	SO:1000183	uninverted_interchromosomal_transposition	SO:0000240
5	"" []	\N	chromosome_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1260033	SO:1000158	SO:1000183	inverted_intrachromosomal_transposition	SO:0000240
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1167432	SO:1000158	SO:1000037	inverted_intrachromosomal_transposition	SO:1000183
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1167433	SO:1000158	SO:1000031	inverted_intrachromosomal_transposition	SO:1000183
5	"" []	\N	chromosome_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1260034	SO:1000159	SO:1000183	uninverted_intrachromosomal_transposition	SO:0000240
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1167436	SO:1000159	SO:1000037	uninverted_intrachromosomal_transposition	SO:1000183
4	"" []	\N	chromosome_variation	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1167437	SO:1000160	SO:1000183	unoriented_insertional_duplication	SO:0000240
4	"" []	\N	chromosome_variation	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1167438	SO:1000161	SO:1000183	unoriented_interchromosomal_transposition	SO:0000240
5	"" []	\N	chromosome_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1260035	SO:1000162	SO:1000183	unoriented_intrachromosomal_transposition	SO:0000240
4	"" []	\N	chromosome_structure_variation	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1167441	SO:1000162	SO:1000037	unoriented_intrachromosomal_transposition	SO:1000183
4	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	1167442	SO:1000170	SO:0001507	uncharacterised_chromosomal_mutation	SO:0001260
4	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"" []	SO	1167443	SO:1000170	SO:0001524	uncharacterised_chromosomal_mutation	SO:0001506
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	1260036	SO:1000171	SO:0000240	deficient_inversion	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	1260037	SO:1000171	SO:0000240	deficient_inversion	SO:0001524
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR	sequence_feature	SOFA	SOFA	sequence	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	SO	1167446	SO:1000173	SO:0001059	tandem_duplication	SO:0000110
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	DBVAR	region	SOFA	SOFA	sequence	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	SO	1167447	SO:1000173	SO:0001411	tandem_duplication	SO:0000001
4	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"" []	SO	1167448	SO:1000175	SO:0000240	partially_characterised_chromosomal_mutation	SO:0001507
4	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"" []	SO	1167449	SO:1000175	SO:0000240	partially_characterised_chromosomal_mutation	SO:0001524
4	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	1167450	SO:1000182	SO:0001506	chromosome_number_variation	SO:0001026
4	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"" []	SO	1167451	SO:1000183	SO:0001506	chromosome_structure_variation	SO:0001026
4	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is alternatively spliced." [SO:xp]	SO	1167452	SO:1001187	SO:0001411	alternatively_spliced_transcript	SO:0000001
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]	SO	1167453	SO:1001188	SO:0000733	encodes_1_polypeptide	SO:0000400
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]	SO	1167454	SO:1001189	SO:0000733	encodes_greater_than_1_polypeptide	SO:0000400
4	"" []	\N	gene_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]	SO	1167455	SO:1001190	SO:0000463	encodes_different_polypeptides_different_stop	SO:0000401
4	"" []	\N	gene_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]	SO	1167456	SO:1001191	SO:0000463	encodes_overlapping_peptides_different_start	SO:0000401
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]	SO	1167457	SO:1001192	SO:0000401	encodes_disjoint_polypeptides	SO:0000733
4	"" []	\N	gene_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]	SO	1167458	SO:1001193	SO:0000463	encodes_overlapping_polypeptides_different_start_and_stop	SO:0000401
4	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	SO	1167459	SO:1001195	SO:0000401	encodes_overlapping_peptides	SO:0000733
4	"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]	\N	gene	SOFA	\N	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	1167460	SO:1001196	SO:0000088	cryptogene	SO:0000704
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	1167461	SO:1001196	SO:0001235	cryptogene	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	1679634	SO:1001196	SO:0001411	cryptogene	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	1260038	SO:1001197	SO:0000831	dicistronic_primary_transcript	SO:0001411
4	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1167464	SO:1001217	SO:0000733	member_of_regulon	SO:0000400
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	1167465	SO:1001246	SO:0000234	CDS_independently_known	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	1167466	SO:1001246	SO:0000834	CDS_independently_known	SO:0000833
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	1167467	SO:1001247	SO:0000836	orphan_CDS	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	1167468	SO:1001247	SO:0000836	orphan_CDS	SO:0000834
5	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	1260039	SO:1001249	SO:0000836	CDS_supported_by_domain_match_data	SO:0000234
5	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	1260040	SO:1001249	SO:0000836	CDS_supported_by_domain_match_data	SO:0000834
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	1260041	SO:1001251	SO:0000234	CDS_supported_by_sequence_similarity_data	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	1260042	SO:1001251	SO:0000834	CDS_supported_by_sequence_similarity_data	SO:0000833
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	1167474	SO:1001254	SO:0000234	CDS_predicted	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	1167475	SO:1001254	SO:0000834	CDS_predicted	SO:0000833
5	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	1260043	SO:1001259	SO:0000836	CDS_supported_by_EST_or_cDNA_data	SO:0000234
5	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	1260044	SO:1001259	SO:0000836	CDS_supported_by_EST_or_cDNA_data	SO:0000834
4	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	\N	UTR	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	1167479	SO:1001260	SO:0000204	internal_Shine_Dalgarno_sequence	SO:0000203
7	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2102399	SO:1001260	SO:0000234	internal_Shine_Dalgarno_sequence	SO:0000233
7	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2102400	SO:1001260	SO:0000834	internal_Shine_Dalgarno_sequence	SO:0000833
4	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	1167484	SO:1001261	SO:0000673	recoded_mRNA	SO:0000831
4	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a translational frameshift of -1." [SO:ke]	SO	1167485	SO:1001262	SO:0000863	minus_1_translationally_frameshifted	SO:0000237
4	"" []	\N	transcript_attribute	\N	\N	sequence	"An attribute describing a translational frameshift of +1." [SO:ke]	SO	1167486	SO:1001263	SO:0000863	plus_1_translationally_frameshifted	SO:0000237
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	1260047	SO:1001264	SO:0000673	mRNA_recoded_by_translational_bypass	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	1260048	SO:1001265	SO:0000673	mRNA_recoded_by_codon_redefinition	SO:0000831
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	1167489	SO:1001268	SO:0000233	recoding_stimulatory_region	SO:0000673
4	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	1167490	SO:1001268	SO:0000833	recoding_stimulatory_region	SO:0000673
4	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	1167491	SO:1001268	SO:0000833	recoding_stimulatory_region	SO:0001411
4	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	1167492	SO:1001269	SO:0000360	four_bp_start_codon	SO:0000851
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	1167493	SO:1001271	SO:0000835	archaeal_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	1167494	SO:1001271	SO:0000835	archaeal_intron	SO:0000833
4	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1167495	SO:1001272	SO:0000835	tRNA_intron	SO:0000185
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1167496	SO:1001272	SO:0000835	tRNA_intron	SO:0000833
4	"A region of a CDS." [SO:cb]	\N	CDS_region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	1167497	SO:1001273	SO:0000360	CTG_start_codon	SO:0000851
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	1167498	SO:1001274	SO:0000234	SECIS_element	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	1167499	SO:1001274	SO:0000834	SECIS_element	SO:0000833
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	1167500	SO:1001277	SO:0000234	three_prime_recoding_site	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	1167501	SO:1001277	SO:0000834	three_prime_recoding_site	SO:0000833
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	1167502	SO:1001279	SO:0000836	three_prime_stem_loop_structure	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	1167503	SO:1001279	SO:0000836	three_prime_stem_loop_structure	SO:0000834
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	1167504	SO:1001280	SO:0000234	five_prime_recoding_site	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	1167505	SO:1001280	SO:0000834	five_prime_recoding_site	SO:0000833
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	1167506	SO:1001281	SO:0000836	flanking_three_prime_quadruplet_recoding_signal	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	1167507	SO:1001281	SO:0000836	flanking_three_prime_quadruplet_recoding_signal	SO:0000834
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	1167508	SO:1001282	SO:0000836	UAG_stop_codon_signal	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	1167509	SO:1001282	SO:0000836	UAG_stop_codon_signal	SO:0000834
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	1167510	SO:1001283	SO:0000836	UAA_stop_codon_signal	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	1167511	SO:1001283	SO:0000836	UAA_stop_codon_signal	SO:0000834
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]	SO	1167512	SO:1001284	SO:0000001	regulon	SO:0000110
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	1167513	SO:1001285	SO:0000836	UGA_stop_codon_signal	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	1167514	SO:1001285	SO:0000836	UGA_stop_codon_signal	SO:0000834
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	1167515	SO:1001286	SO:0000836	three_prime_repeat_recoding_signal	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	1167516	SO:1001286	SO:0000836	three_prime_repeat_recoding_signal	SO:0000834
4	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	1167517	SO:1001287	SO:0000836	distant_three_prime_recoding_signal	SO:0000234
4	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	1167518	SO:1001287	SO:0000836	distant_three_prime_recoding_signal	SO:0000834
4	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	1167519	SO:1001288	SO:0000234	stop_codon_signal	SO:0000233
4	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	1167520	SO:1001288	SO:0000834	stop_codon_signal	SO:0000833
4	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]	SO	1167521	SO:2000061	SO:0000001	databank_entry	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]	SO	1260049	SO:3000000	SO:0000001	gene_segment	SO:0000110
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1639717	SO:0000004	SO:0000673	interior_coding_exon	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"" []	SO	2441012	SO:0000004	SO:0001411	interior_coding_exon	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639719	SO:0000005	SO:0000001	satellite_DNA	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]	SO	2899070	SO:0000007	SO:0000001	read_pair	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	SO	1639722	SO:0000012	SO:0000831	scRNA_primary_transcript	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SO	1639723	SO:0000013	SO:0000831	scRNA	SO:0001411
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	1639724	SO:0000014	SO:0000714	INR_motif	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	1639725	SO:0000014	SO:0000167	INR_motif	SO:0001055
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	1639726	SO:0000015	SO:0000714	DPE_motif	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	1639727	SO:0000015	SO:0000167	DPE_motif	SO:0001055
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	1639728	SO:0000016	SO:0000714	BREu_motif	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	1639729	SO:0000016	SO:0000167	BREu_motif	SO:0001055
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	2441021	SO:0000017	SO:0001411	PSE_motif	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	1639731	SO:0000017	SO:0005836	PSE_motif	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	SO	1639732	SO:0000020	SO:0001411	RNA_internal_loop	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	SO	1639733	SO:0000021	SO:0001683	asymmetric_RNA_internal_loop	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]	SO	1639734	SO:0000022	SO:0001411	A_minor_RNA_motif	SO:0000001
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	1639735	SO:0000023	SO:0000714	K_turn_RNA_motif	SO:0001683
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	1639736	SO:0000024	SO:0000714	sarcin_like_RNA_motif	SO:0001683
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	SO	1639737	SO:0000025	SO:0001683	symmetric_RNA_internal_loop	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1639738	SO:0000026	SO:0001411	RNA_junction_loop	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1639739	SO:0000027	SO:0001683	RNA_hook_turn	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]	SO	1639740	SO:0000029	SO:0000001	WC_base_pair	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A type of non-canonical base-pairing." [PMID:12177293]	SO	1639741	SO:0000030	SO:0000001	sugar_edge_base_pair	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	1639742	SO:0000031	SO:0000001	aptamer	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]	SO	1639743	SO:0000032	SO:0001409	DNA_aptamer	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	1639744	SO:0000033	SO:0001409	RNA_aptamer	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]	SO	1639745	SO:0000034	SO:0001409	morpholino_oligo	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	2279360	SO:0000035	SO:0001411	riboswitch	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	1805583	SO:0000035	SO:0000831	riboswitch	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	1639748	SO:0000036	SO:0001235	matrix_attachment_site	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]	SO	2165091	SO:0000036	SO:0000001	matrix_attachment_site	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	1639750	SO:0000037	SO:0005836	locus_control_region	SO:0000831
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A clone of a DNA region of a genome." [SO:ma]	SO	1639751	SO:0000040	SO:0000001	genomic_clone	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A pseudogene caused by unequal crossing over at recombination." [SO:ke]	SO	1639752	SO:0000044	SO:0000001	pseudogene_by_unequal_crossing_over	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]	SO	1639753	SO:0000051	SO:0000001	probe	SO:0000110
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	1639754	SO:0000054	SO:0001506	aneuploid	SO:0001026
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	1639755	SO:0000055	SO:0001507	hyperploid	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	1639756	SO:0000055	SO:0001524	hyperploid	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	1639757	SO:0000056	SO:0001507	hypoploid	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	1639758	SO:0000056	SO:0001524	hypoploid	SO:0001506
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SO	1639759	SO:0000057	SO:0000831	operator	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SO	1639760	SO:0000059	SO:0001411	nuclease_binding_site	SO:0000001
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	1639761	SO:0000060	SO:0001507	compound_chromosome_arm	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"" []	SO	1639762	SO:0000060	SO:0001524	compound_chromosome_arm	SO:0001506
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	SO	1639763	SO:0000061	SO:0000409	restriction_enzyme_binding_site	SO:0001411
6	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	1805584	SO:0000062	SO:0000240	deficient_intrachromosomal_transposition	SO:0001507
6	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	1805585	SO:0000062	SO:0000240	deficient_intrachromosomal_transposition	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	1639766	SO:0000063	SO:0000240	deficient_interchromosomal_transposition	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	1639767	SO:0000063	SO:0000240	deficient_interchromosomal_transposition	SO:0001524
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	1639768	SO:0000065	SO:0001506	free_chromosome_arm	SO:0001026
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]	SO	1639769	SO:0000069	SO:0000733	inside_intron	SO:0000400
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]	SO	1639770	SO:0000070	SO:0000401	inside_intron_antiparallel	SO:0000733
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]	SO	1639771	SO:0000071	SO:0000401	inside_intron_parallel	SO:0000733
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]	SO	1639772	SO:0000073	SO:0000733	five_prime_three_prime_overlap	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]	SO	1639773	SO:0000074	SO:0000733	five_prime_five_prime_overlap	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]	SO	1639774	SO:0000075	SO:0000733	three_prime_three_prime_overlap	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]	SO	1639775	SO:0000076	SO:0000733	three_prime_five_prime_overlap	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]	SO	1639776	SO:0000077	SO:0000733	antisense	SO:0000400
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is polycistronic." [SO:xp]	SO	1639777	SO:0000078	SO:0000001	polycistronic_transcript	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is dicistronic." [SO:ke]	SO	1805586	SO:0000079	SO:0000001	dicistronic_transcript	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene located in kinetoplast sequence." [SO:xp]	SO	1639779	SO:0000089	SO:0000001	kinetoplast_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from apicoplast sequence." [SO:xp]	SO	1639780	SO:0000091	SO:0000001	apicoplast_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from chloroplast sequence." [SO:xp]	SO	1639781	SO:0000092	SO:0000001	ct_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from chromoplast_sequence." [SO:xp]	SO	1639782	SO:0000093	SO:0000001	chromoplast_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from cyanelle sequence." [SO:xp]	SO	1639783	SO:0000094	SO:0000001	cyanelle_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A plastid gene from leucoplast sequence." [SO:xp]	SO	1639784	SO:0000095	SO:0000001	leucoplast_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene from proplastid sequence." [SO:ke]	SO	1639785	SO:0000096	SO:0000001	proplastid_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A proviral gene with origin endogenous retrovirus." [SO:xp]	SO	1639786	SO:0000100	SO:0000001	endogenous_retroviral_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A match to an EST or cDNA sequence." [SO:ke]	SO	1639788	SO:0000102	SO:0000001	expressed_sequence_match	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The end of the clone insert." [SO:ke]	SO	1805587	SO:0000103	SO:0000001	clone_insert_end	SO:0000110
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"" []	SO	1639791	SO:0000107	SO:0000695	sequencing_primer	SO:0001409
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA with a frameshift." [SO:xp]	SO	1639792	SO:0000108	SO:0000831	mRNA_with_frameshift	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	SO	1639795	SO:0000112	SO:0001409	primer	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	1639797	SO:0000114	SO:0001411	methylated_cytosine	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript with a translational frameshift." [SO:xp]	SO	1639798	SO:0000118	SO:0000001	transcript_with_translational_frameshift	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	SO	1639799	SO:0000120	SO:0001411	protein_coding_primary_transcript	SO:0000001
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	1639800	SO:0000121	SO:0000695	forward_primer	SO:0001409
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]	SO	1639801	SO:0000124	SO:0000733	transcriptionally_constitutive	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An inducer molecule is required for transcription to occur." [SO:ke]	SO	1639802	SO:0000125	SO:0000733	transcriptionally_induced	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A repressor molecule is required for transcription to stop." [SO:ke]	SO	1639803	SO:0000126	SO:0000733	transcriptionally_repressed	SO:0000400
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is silenced by DNA methylation." [SO:xp]	SO	1805588	SO:0000129	SO:0000001	gene_silenced_by_DNA_methylation	SO:0000110
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	1639805	SO:0000132	SO:0000695	reverse_primer	SO:0001409
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	1639806	SO:0000135	SO:0000733	maternally_imprinted	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]	SO	1639807	SO:0000136	SO:0000733	paternally_imprinted	SO:0000400
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An epigenetically modified gene, rearranged at the DNA level." [SO:xp]	SO	1639808	SO:0000138	SO:0000001	gene_rearranged_at_DNA_level	SO:0000110
7	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	2165092	SO:0000139	SO:0000673	ribosome_entry_site	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	2806600	SO:0000139	SO:0001411	ribosome_entry_site	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	1805589	SO:0000140	SO:0001411	attenuator	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1805590	SO:0000141	SO:0000001	terminator	SO:0000110
6	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	1805591	SO:0000145	SO:0000234	recoded_codon	SO:0000233
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	1805592	SO:0000145	SO:0000834	recoded_codon	SO:0000833
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	1805593	SO:0000148	SO:0001410	supercontig	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	1639823	SO:0000152	SO:0001409	YAC	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]	SO	2080965	SO:0000152	SO:0000001	YAC	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	1639825	SO:0000153	SO:0001409	BAC	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]	SO	2080966	SO:0000153	SO:0000001	BAC	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	1639827	SO:0000154	SO:0001409	PAC	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	SO	2080967	SO:0000154	SO:0000001	PAC	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	1639829	SO:0000156	SO:0001409	cosmid	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]	SO	2080968	SO:0000156	SO:0000001	cosmid	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	1639831	SO:0000157	SO:0001409	phagemid	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]	SO	2080969	SO:0000157	SO:0000001	phagemid	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	1639833	SO:0000158	SO:0001409	fosmid	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cloning vector that utilizes the E. coli F factor." [SO:ma]	SO	2080970	SO:0000158	SO:0000001	fosmid	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	1639835	SO:0000161	SO:0001411	methylated_adenine	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	1639836	SO:0000162	SO:0000831	splice_site	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]	SO	2165095	SO:0000162	SO:0000001	splice_site	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1639838	SO:0000163	SO:0000185	five_prime_cis_splice_site	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1639839	SO:0000163	SO:0000833	five_prime_cis_splice_site	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1639840	SO:0000163	SO:0000833	five_prime_cis_splice_site	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1639841	SO:0000164	SO:0000185	three_prime_cis_splice_site	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1639842	SO:0000164	SO:0000833	three_prime_cis_splice_site	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	1639843	SO:0000164	SO:0000833	three_prime_cis_splice_site	SO:0001411
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639844	SO:0000165	SO:0005836	enhancer	SO:0000831
5	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"An enhancer bound by a factor." [SO:xp]	SO	1639845	SO:0000166	SO:0001679	enhancer_bound_by_factor	SO:0005836
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SO	1639846	SO:0000167	SO:0000831	promoter	SO:0001411
5	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	1639847	SO:0000169	SO:0001679	RNApol_I_promoter	SO:0005836
5	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	1639848	SO:0000170	SO:0001679	RNApol_II_promoter	SO:0005836
5	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	1639849	SO:0000171	SO:0001679	RNApol_III_promoter	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2885614	SO:0000172	SO:0001411	CAAT_signal	SO:0000001
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639851	SO:0000172	SO:0001055	CAAT_signal	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639852	SO:0000173	SO:0001683	GC_rich_promoter_region	SO:0001411
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639853	SO:0000173	SO:0001055	GC_rich_promoter_region	SO:0001679
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	1639854	SO:0000174	SO:0000714	TATA_box	SO:0001683
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2961201	SO:0000175	SO:0001411	minus_10_signal	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441056	SO:0000175	SO:0001679	minus_10_signal	SO:0005836
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639857	SO:0000175	SO:0000167	minus_10_signal	SO:0001055
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2961202	SO:0000176	SO:0001411	minus_35_signal	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441058	SO:0000176	SO:0001679	minus_35_signal	SO:0005836
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639860	SO:0000176	SO:0000167	minus_35_signal	SO:0001055
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A nucleotide match against a sequence from another organism." [SO:ma]	SO	1639861	SO:0000177	SO:0000001	cross_genome_match	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The start of the clone insert." [SO:ke]	SO	1805595	SO:0000179	SO:0000001	clone_insert_start	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	SO	2080994	SO:0000180	SO:0000001	retrotransposon	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	SO	1639864	SO:0000180	SO:0001411	retrotransposon	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A match against a translated sequence." [SO:ke]	SO	1639865	SO:0000181	SO:0000001	translated_nucleotide_match	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	SO	2080995	SO:0000182	SO:0000001	DNA_transposon	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]	SO	1639867	SO:0000182	SO:0001411	DNA_transposon	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	1639868	SO:0000184	SO:0000185	U2_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	1639869	SO:0000184	SO:0000833	U2_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	1639870	SO:0000184	SO:0000833	U2_intron	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A transcript that in its initial state requires modification to be functional." [SO:ma]	SO	1639871	SO:0000185	SO:0000001	primary_transcript	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	1639872	SO:0000186	SO:0001037	LTR_retrotransposon	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	1639873	SO:0000186	SO:0001037	LTR_retrotransposon	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639874	SO:0000188	SO:0000831	intron	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2165096	SO:0000188	SO:0000001	intron	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	1639876	SO:0000189	SO:0001037	non_LTR_retrotransposon	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	1639877	SO:0000189	SO:0001037	non_LTR_retrotransposon	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1639878	SO:0000190	SO:0000673	five_prime_intron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441063	SO:0000190	SO:0001411	five_prime_intron	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1639880	SO:0000191	SO:0000673	interior_intron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441064	SO:0000191	SO:0001411	interior_intron	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1639882	SO:0000192	SO:0000673	three_prime_intron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441065	SO:0000192	SO:0001411	three_prime_intron	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]	SO	1639884	SO:0000193	SO:0000001	RFLP_fragment	SO:0000110
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	1639885	SO:0000194	SO:0001039	LINE_element	SO:0001037
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	1639886	SO:0000195	SO:0000831	coding_exon	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]	SO	2165097	SO:0000195	SO:0000001	coding_exon	SO:0000110
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	1805596	SO:0000196	SO:0000673	five_prime_coding_exon_coding_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	2625326	SO:0000196	SO:0001411	five_prime_coding_exon_coding_region	SO:0000001
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	1805598	SO:0000197	SO:0000673	three_prime_coding_exon_coding_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	2625327	SO:0000197	SO:0001411	three_prime_coding_exon_coding_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An exon that does not contain any codons." [SO:ke]	SO	1639896	SO:0000198	SO:0000831	noncoding_exon	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An exon that does not contain any codons." [SO:ke]	SO	2165098	SO:0000198	SO:0000001	noncoding_exon	SO:0000110
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	1639898	SO:0000200	SO:0000673	five_prime_coding_exon	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	2441070	SO:0000200	SO:0001411	five_prime_coding_exon	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	1639900	SO:0000201	SO:0000831	interior_exon	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]	SO	2165099	SO:0000201	SO:0000001	interior_exon	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	1639902	SO:0000202	SO:0000673	three_prime_coding_exon	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	2441071	SO:0000202	SO:0001411	three_prime_coding_exon	SO:0000001
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	1639904	SO:0000203	SO:0000673	UTR	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	2441072	SO:0000203	SO:0001411	UTR	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639906	SO:0000204	SO:0000233	five_prime_UTR	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639907	SO:0000204	SO:0000833	five_prime_UTR	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639908	SO:0000204	SO:0000833	five_prime_UTR	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639909	SO:0000205	SO:0000233	three_prime_UTR	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639910	SO:0000205	SO:0000833	three_prime_UTR	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639911	SO:0000205	SO:0000833	three_prime_UTR	SO:0001411
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	1639912	SO:0000206	SO:0001039	SINE_element	SO:0001037
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1639913	SO:0000207	SO:0000001	simple_sequence_length_variation	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	1639914	SO:0000208	SO:0001037	terminal_inverted_repeat_element	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	1639915	SO:0000208	SO:0001037	terminal_inverted_repeat_element	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SO	1639916	SO:0000209	SO:0000831	rRNA_primary_transcript	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	SO	1639917	SO:0000210	SO:0000831	tRNA_primary_transcript	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	1639918	SO:0000211	SO:0000673	alanine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	1639919	SO:0000212	SO:0000673	arginine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	1639920	SO:0000213	SO:0000673	asparagine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	1639921	SO:0000214	SO:0000673	aspartic_acid_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	1639922	SO:0000215	SO:0000673	cysteine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	1639923	SO:0000216	SO:0000673	glutamic_acid_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	1639924	SO:0000217	SO:0000673	glutamine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	1639925	SO:0000218	SO:0000673	glycine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	1639926	SO:0000219	SO:0000673	histidine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	1639927	SO:0000220	SO:0000673	isoleucine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	1639928	SO:0000221	SO:0000673	leucine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	1639929	SO:0000222	SO:0000673	lysine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	1639930	SO:0000223	SO:0000673	methionine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	1639931	SO:0000224	SO:0000673	phenylalanine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	1639932	SO:0000225	SO:0000673	proline_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	1639933	SO:0000226	SO:0000673	serine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	1639934	SO:0000227	SO:0000673	threonine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	1639935	SO:0000228	SO:0000673	tryptophan_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	1639936	SO:0000229	SO:0000673	tyrosine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	1639937	SO:0000230	SO:0000673	valine_tRNA_primary_transcript	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	SO	1639938	SO:0000231	SO:0000831	snRNA_primary_transcript	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	SO	1639939	SO:0000232	SO:0000831	snoRNA_primary_transcript	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SO	1639940	SO:0000233	SO:0000001	mature_transcript	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SO	1639941	SO:0000234	SO:0001411	mRNA	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	1639942	SO:0000235	SO:0001411	TF_binding_site	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	1639943	SO:0000238	SO:0001037	foldback_element	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	1639944	SO:0000238	SO:0001037	foldback_element	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	1639945	SO:0000241	SO:0000233	internal_UTR	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	1639946	SO:0000241	SO:0000833	internal_UTR	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	1639947	SO:0000241	SO:0000833	internal_UTR	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	1639948	SO:0000242	SO:0000233	untranslated_region_polycistronic_mRNA	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	1639949	SO:0000242	SO:0000833	untranslated_region_polycistronic_mRNA	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	1639950	SO:0000242	SO:0000833	untranslated_region_polycistronic_mRNA	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	2165100	SO:0000243	SO:0000233	internal_ribosome_entry_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	2165101	SO:0000243	SO:0000833	internal_ribosome_entry_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	2165102	SO:0000243	SO:0000833	internal_ribosome_entry_site	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SO	1639956	SO:0000252	SO:0000831	rRNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SO	1639957	SO:0000253	SO:0000831	tRNA	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	1639958	SO:0000254	SO:0000673	alanyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	1639959	SO:0000255	SO:0000673	rRNA_small_subunit_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	1639960	SO:0000256	SO:0000673	asparaginyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	1639961	SO:0000257	SO:0000673	aspartyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	1639962	SO:0000258	SO:0000673	cysteinyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	1639963	SO:0000259	SO:0000673	glutaminyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	1639964	SO:0000260	SO:0000673	glutamyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	1639965	SO:0000261	SO:0000673	glycyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	1639966	SO:0000262	SO:0000673	histidyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	1639967	SO:0000263	SO:0000673	isoleucyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	1639968	SO:0000264	SO:0000673	leucyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	1639969	SO:0000265	SO:0000673	lysyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	1639970	SO:0000266	SO:0000673	methionyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	1639971	SO:0000267	SO:0000673	phenylalanyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	1639972	SO:0000268	SO:0000673	prolyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	1639973	SO:0000269	SO:0000673	seryl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	1639974	SO:0000270	SO:0000673	threonyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	1639975	SO:0000271	SO:0000673	tryptophanyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	1639976	SO:0000272	SO:0000673	tyrosyl_tRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	1639977	SO:0000273	SO:0000673	valyl_tRNA	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SO	1639978	SO:0000274	SO:0000831	snRNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SO	1639979	SO:0000275	SO:0000831	snoRNA	SO:0001411
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	1639980	SO:0000276	SO:0000673	miRNA	SO:0000831
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is bound by a nucleic acid." [SO:xp]	SO	1639981	SO:0000278	SO:0000001	transcript_bound_by_nucleic_acid	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is bound by a protein." [SO:xp]	SO	1639982	SO:0000279	SO:0000001	transcript_bound_by_protein	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	1639984	SO:0000282	SO:0000673	mRNA_with_minus_1_frameshift	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	1639985	SO:0000283	SO:0001037	engineered_foreign_transposable_element_gene	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	1639986	SO:0000283	SO:0001037	engineered_foreign_transposable_element_gene	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [SO:xp]	SO	1639988	SO:0000283	SO:0001409	engineered_foreign_transposable_element_gene	SO:0000001
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1639989	SO:0000286	SO:0001039	long_terminal_repeat	SO:0001037
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	SO	1639991	SO:0000289	SO:0001411	microsatellite	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1639992	SO:0000290	SO:0000657	dinucleotide_repeat_microsatellite_feature	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1639993	SO:0000291	SO:0000657	trinucleotide_repeat_microsatellite_feature	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	1639995	SO:0000295	SO:0000185	U12_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	1639996	SO:0000295	SO:0000833	U12_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	1639997	SO:0000295	SO:0000833	U12_intron	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1639998	SO:0000299	SO:0000001	specific_recombination_site	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1639999	SO:0000300	SO:0001411	recombination_feature_of_rearranged_gene	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	1640000	SO:0000301	SO:0000298	vertebrate_immune_system_gene_recombination_feature	SO:0001411
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640001	SO:0000302	SO:0000299	J_gene_recombination_feature	SO:0000669
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	1640002	SO:0000303	SO:0000831	clip	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Part of the primary transcript that is clipped off during processing." [SO:ke]	SO	2165104	SO:0000303	SO:0000001	clip	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A nucleotide modified by methylation." [SO:ke]	SO	1640004	SO:0000306	SO:0000001	methylated_DNA_base_feature	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640005	SO:0000313	SO:0000001	stem_loop	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	1640006	SO:0000315	SO:0000831	TSS	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]	SO	2165105	SO:0000315	SO:0000001	TSS	SO:0000110
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	1640008	SO:0000316	SO:0000673	CDS	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	2441145	SO:0000316	SO:0001411	CDS	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	SO	1640010	SO:0000317	SO:0000001	cDNA_clone	SO:0000110
6	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	1805601	SO:0000318	SO:0000234	start_codon	SO:0000233
6	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	1805602	SO:0000318	SO:0000834	start_codon	SO:0000833
6	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	1805603	SO:0000319	SO:0000234	stop_codon	SO:0000233
6	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	1805604	SO:0000319	SO:0000834	stop_codon	SO:0000833
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	1640019	SO:0000320	SO:0005836	intronic_splice_enhancer	SO:0000831
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	2165106	SO:0000320	SO:0000673	intronic_splice_enhancer	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	2806613	SO:0000320	SO:0001411	intronic_splice_enhancer	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	1640024	SO:0000321	SO:0000673	mRNA_with_plus_1_frameshift	SO:0000831
5	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"" []	SO	1640025	SO:0000322	SO:0000410	nuclease_hypersensitive_site	SO:0000409
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	1805605	SO:0000323	SO:0000233	coding_start	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	1805606	SO:0000323	SO:0000833	coding_start	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	1805607	SO:0000323	SO:0000833	coding_start	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]	SO	1640029	SO:0000324	SO:0000001	tag	SO:0000110
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	1640030	SO:0000325	SO:0000673	rRNA_large_subunit_primary_transcript	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	SO	1640031	SO:0000326	SO:0001409	SAGE_tag	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	1805608	SO:0000327	SO:0000233	coding_end	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	1805609	SO:0000327	SO:0000833	coding_end	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	1805610	SO:0000327	SO:0000833	coding_end	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640035	SO:0000328	SO:0001409	microarray_oligo	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	1640036	SO:0000329	SO:0000673	mRNA_with_plus_2_frameshift	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]	SO	1640037	SO:0000331	SO:0001409	STS	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	1640038	SO:0000333	SO:0001411	exon_junction	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	1640039	SO:0000335	SO:0000673	mRNA_with_minus_2_frameshift	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]	SO	1640040	SO:0000337	SO:0001409	RNAi_reagent	SO:0000001
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	1640041	SO:0000338	SO:0001039	MITE	SO:0001037
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640043	SO:0000342	SO:0001411	site_specific_recombination_target_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Region of a transcript that regulates splicing." [SO:ke]	SO	1640044	SO:0000344	SO:0000831	splice_enhancer	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	SO	1640045	SO:0000345	SO:0001409	EST	SO:0000001
5	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	1640046	SO:0000346	SO:0000669	loxP_site	SO:0000298
5	"" []	\N	recombination_feature	\N	\N	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	1640047	SO:0000350	SO:0000669	FRT_site	SO:0000298
5	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	1640048	SO:0000354	SO:0000410	group_1_intron_homing_endonuclease_target_region	SO:0000409
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	1805611	SO:0000360	SO:0000233	codon	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	1805612	SO:0000360	SO:0000833	codon	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	1805613	SO:0000360	SO:0000833	codon	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transgene that is floxed." [SO:xp]	SO	1640052	SO:0000363	SO:0000001	floxed_gene	SO:0000110
5	"" []	\N	recombination_feature	\N	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	1640054	SO:0000367	SO:0000669	attI_site	SO:0000298
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	2548775	SO:0000367	SO:0000001	attI_site	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	2441167	SO:0000367	SO:0001411	attI_site	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SO	1640057	SO:0000370	SO:0000831	small_regulatory_ncRNA	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	1640058	SO:0000371	SO:0001037	conjugative_transposon	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	1640059	SO:0000371	SO:0001037	conjugative_transposon	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]	SO	1640060	SO:0000372	SO:0000001	enzymatic_RNA	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recombinationally rearranged gene by inversion." [SO:xp]	SO	1640061	SO:0000373	SO:0000001	recombinationally_inverted_gene	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An RNA with catalytic activity." [SO:ma]	SO	1640062	SO:0000374	SO:0001411	ribozyme	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	1640063	SO:0000375	SO:0000233	rRNA_5_8S	SO:0000673
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	1640064	SO:0000376	SO:0000673	RNA_6S	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	1640065	SO:0000377	SO:0000673	CsrB_RsmB_RNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	1640066	SO:0000378	SO:0000673	DsrA_RNA	SO:0000831
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	1640067	SO:0000379	SO:0000233	GcvB_RNA	SO:0000673
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]	SO	1640068	SO:0000380	SO:0001411	hammerhead_ribozyme	SO:0000001
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	1640069	SO:0000381	SO:0000835	group_IIA_intron	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	1640070	SO:0000381	SO:0000835	group_IIA_intron	SO:0000833
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"" []	SO	1640071	SO:0000382	SO:0000835	group_IIB_intron	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"" []	SO	1640072	SO:0000382	SO:0000835	group_IIB_intron	SO:0000833
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	1640073	SO:0000383	SO:0000673	MicF_RNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	1640074	SO:0000384	SO:0000673	OxyS_RNA	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SO	1640075	SO:0000385	SO:0000831	RNase_MRP_RNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SO	1640076	SO:0000386	SO:0000831	RNase_P_RNA	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	1640077	SO:0000387	SO:0000673	RprA_RNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	1640078	SO:0000388	SO:0000673	RRE_RNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	1640079	SO:0000389	SO:0000673	spot_42_RNA	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SO	1640080	SO:0000390	SO:0000831	telomerase_RNA	SO:0001411
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	1640081	SO:0000391	SO:0000673	U1_snRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	1640082	SO:0000392	SO:0000673	U2_snRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	1640083	SO:0000393	SO:0000673	U4_snRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	1640084	SO:0000394	SO:0000673	U4atac_snRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	1640085	SO:0000395	SO:0000673	U5_snRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	1640086	SO:0000396	SO:0000673	U6_snRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	1640087	SO:0000397	SO:0000673	U6atac_snRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	1640088	SO:0000398	SO:0000673	U11_snRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	1640089	SO:0000399	SO:0000673	U12_snRNA	SO:0000831
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	1640090	SO:0000403	SO:0000233	U14_snoRNA	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SO	1640091	SO:0000404	SO:0000831	vault_RNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SO	1640092	SO:0000405	SO:0000831	Y_RNA	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	1640093	SO:0000406	SO:0000673	twintron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	2441199	SO:0000406	SO:0001411	twintron	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	1640095	SO:0000407	SO:0000233	rRNA_18S	SO:0000673
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]	SO	1805614	SO:0000417	SO:0000001	polypeptide_domain	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens,SOFA	sequence_feature	SOFA	SOFA	sequence	"The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2486343	SO:0000418	SO:0000001	signal_peptide	SO:0000110
5	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	1640101	SO:0000420	SO:0000101	five_prime_terminal_inverted_repeat	SO:0001039
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706567	SO:0000420	SO:0001411	five_prime_terminal_inverted_repeat	SO:0000001
5	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	1640103	SO:0000421	SO:0000101	three_prime_terminal_inverted_repeat	SO:0001039
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706569	SO:0000421	SO:0001411	three_prime_terminal_inverted_repeat	SO:0000001
5	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1640105	SO:0000422	SO:0000180	U5_LTR_region	SO:0000101
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885626	SO:0000422	SO:0001411	U5_LTR_region	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2917074	SO:0000422	SO:0000001	U5_LTR_region	SO:0000110
5	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1640108	SO:0000423	SO:0000180	R_LTR_region	SO:0000101
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885628	SO:0000423	SO:0001411	R_LTR_region	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2917075	SO:0000423	SO:0000001	R_LTR_region	SO:0000110
5	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1640111	SO:0000424	SO:0000180	U3_LTR_region	SO:0000101
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885630	SO:0000424	SO:0001411	U3_LTR_region	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2917076	SO:0000424	SO:0000001	U3_LTR_region	SO:0000110
5	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	1640114	SO:0000425	SO:0000101	five_prime_LTR	SO:0001039
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2731400	SO:0000425	SO:0000001	five_prime_LTR	SO:0000110
5	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	1640116	SO:0000426	SO:0000101	three_prime_LTR	SO:0001039
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2731401	SO:0000426	SO:0000001	three_prime_LTR	SO:0000110
5	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1640118	SO:0000427	SO:0000186	R_five_prime_LTR_region	SO:0000180
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640119	SO:0000427	SO:0000657	R_five_prime_LTR_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640120	SO:0000427	SO:0001412	R_five_prime_LTR_region	SO:0000001
5	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1640121	SO:0000428	SO:0000186	U5_five_prime_LTR_region	SO:0000180
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640122	SO:0000428	SO:0000657	U5_five_prime_LTR_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640123	SO:0000428	SO:0001412	U5_five_prime_LTR_region	SO:0000001
5	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1640124	SO:0000429	SO:0000186	U3_five_prime_LTR_region	SO:0000180
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640125	SO:0000429	SO:0000657	U3_five_prime_LTR_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640126	SO:0000429	SO:0001412	U3_five_prime_LTR_region	SO:0000001
5	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1640127	SO:0000430	SO:0000186	R_three_prime_LTR_region	SO:0000180
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640128	SO:0000430	SO:0000657	R_three_prime_LTR_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640129	SO:0000430	SO:0001412	R_three_prime_LTR_region	SO:0000001
5	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1640130	SO:0000431	SO:0000186	U3_three_prime_LTR_region	SO:0000180
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640131	SO:0000431	SO:0000657	U3_three_prime_LTR_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640132	SO:0000431	SO:0001412	U3_three_prime_LTR_region	SO:0000001
5	"A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]	\N	retrotransposon	\N	\N	sequence	"" []	SO	1640133	SO:0000432	SO:0000186	U5_three_prime_LTR_region	SO:0000180
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640134	SO:0000432	SO:0000657	U5_three_prime_LTR_region	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640135	SO:0000432	SO:0001412	U5_three_prime_LTR_region	SO:0000001
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	1640136	SO:0000433	SO:0001039	non_LTR_retrotransposon_polymeric_tract	SO:0001037
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]	SO	1640137	SO:0000434	SO:0000001	target_site_duplication	SO:0000110
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	1640138	SO:0000435	SO:0001039	RR_tract	SO:0001037
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"" []	SO	1640139	SO:0000439	SO:0000240	inverted_ring_chromosome	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"" []	SO	1640140	SO:0000439	SO:0000240	inverted_ring_chromosome	SO:0001524
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A single stranded oligonucleotide." [SO:ke]	SO	1640142	SO:0000441	SO:0000001	ss_oligo	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A double stranded oligonucleotide." [SO:ke]	SO	1640143	SO:0000442	SO:0000001	ds_oligo	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	1640144	SO:0000444	SO:0000673	three_prime_noncoding_exon	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	2441229	SO:0000444	SO:0001411	three_prime_noncoding_exon	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	1640146	SO:0000445	SO:0000673	five_prime_noncoding_exon	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	2441230	SO:0000445	SO:0001411	five_prime_noncoding_exon	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	1640148	SO:0000446	SO:0000673	UTR_intron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	2441231	SO:0000446	SO:0001411	UTR_intron	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	1640150	SO:0000447	SO:0000185	five_prime_UTR_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	1640151	SO:0000447	SO:0000833	five_prime_UTR_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	1640152	SO:0000447	SO:0000833	five_prime_UTR_intron	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	1640153	SO:0000448	SO:0000185	three_prime_UTR_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	1640154	SO:0000448	SO:0000833	three_prime_UTR_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	1640155	SO:0000448	SO:0000833	three_prime_UTR_intron	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes a polyadenylated mRNA." [SO:xp]	SO	1640157	SO:0000451	SO:0000001	gene_with_polyadenylated_mRNA	SO:0000110
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	1640158	SO:0000453	SO:0001506	chromosomal_transposition	SO:0001026
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SO	1640159	SO:0000454	SO:0000831	rasiRNA	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes an mRNA with a frameshift." [SO:xp]	SO	1640160	SO:0000455	SO:0000001	gene_with_mRNA_with_frameshift	SO:0000110
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	1640161	SO:0000457	SO:0001507	interchromosomal_duplication	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	1640162	SO:0000457	SO:0001524	interchromosomal_duplication	SO:0001506
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640163	SO:0000458	SO:0000299	D_gene_segment	SO:0000669
5	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	1640164	SO:0000460	SO:0000669	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000298
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	1640165	SO:0000461	SO:0000240	inversion_derived_bipartite_deficiency	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	1640166	SO:0000461	SO:0000240	inversion_derived_bipartite_deficiency	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	1640167	SO:0000465	SO:0000240	inversion_derived_deficiency_plus_duplication	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	1640168	SO:0000465	SO:0000240	inversion_derived_deficiency_plus_duplication	SO:0001524
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640169	SO:0000466	SO:0000299	V_gene_segment	SO:0000669
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]	SO	1640170	SO:0000467	SO:0000733	post_translationally_regulated_by_protein_stability	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]	SO	1640172	SO:0000469	SO:0000733	post_translationally_regulated_by_protein_modification	SO:0000400
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640173	SO:0000470	SO:0000299	J_gene_segment	SO:0000669
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation." [SO:ke]	SO	1640174	SO:0000471	SO:0000733	autoregulated	SO:0000400
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]	SO	1640175	SO:0000472	SO:0000001	tiling_path	SO:0000110
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	1640176	SO:0000473	SO:0000401	negatively_autoregulated	SO:0000733
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	1640178	SO:0000475	SO:0000401	positively_autoregulated	SO:0000733
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	2899071	SO:0000476	SO:0000001	contig_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	1640180	SO:0000476	SO:0000719	contig_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	2081239	SO:0000476	SO:0001876	contig_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A DNA sequencer read which is part of a contig." [SO:ke]	SO	2486344	SO:0000476	SO:0001248	contig_read	SO:0001410
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640183	SO:0000478	SO:0000299	C_gene_segment	SO:0000669
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is trans-spliced." [SO:xp]	SO	1640184	SO:0000479	SO:0000001	trans_spliced_transcript	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	2165112	SO:0000480	SO:0000001	tiling_path_clone	SO:0000110
5	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]	SO	1640186	SO:0000480	SO:0001248	tiling_path_clone	SO:0001410
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	2486345	SO:0000481	SO:0000001	terminal_inverted_repeat	SO:0000110
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	1640188	SO:0000481	SO:0001039	terminal_inverted_repeat	SO:0001037
5	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	1640189	SO:0000482	SO:0000669	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000298
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A primary transcript that is never translated into a protein." [SO:ke]	SO	1640190	SO:0000483	SO:0001411	nc_primary_transcript	SO:0000001
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	1805617	SO:0000484	SO:0000673	three_prime_coding_exon_noncoding_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	2625338	SO:0000484	SO:0001411	three_prime_coding_exon_noncoding_region	SO:0000001
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640195	SO:0000485	SO:0000299	DJ_J_cluster	SO:0000669
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	1805619	SO:0000486	SO:0000673	five_prime_coding_exon_noncoding_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	2625339	SO:0000486	SO:0001411	five_prime_coding_exon_noncoding_region	SO:0000001
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640200	SO:0000487	SO:0000299	VDJ_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640201	SO:0000488	SO:0000299	VDJ_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640202	SO:0000489	SO:0000299	VJ_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640203	SO:0000490	SO:0000299	VJ_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640204	SO:0000491	SO:0000299	VJ_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1640205	SO:0000492	SO:0000299	D_gene_recombination_feature	SO:0000669
6	"" []	\N	specific_recombination_site	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1805621	SO:0000493	SO:0000300	three_prime_D_heptamer	SO:0000299
6	"" []	\N	specific_recombination_site	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1805622	SO:0000494	SO:0000300	three_prime_D_nonamer	SO:0000299
7	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2165113	SO:0000495	SO:0000299	three_prime_D_spacer	SO:0000669
6	"" []	\N	specific_recombination_site	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1805623	SO:0000496	SO:0000300	five_prime_D_heptamer	SO:0000299
6	"" []	\N	specific_recombination_site	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1805624	SO:0000497	SO:0000300	five_prime_D_nonamer	SO:0000299
7	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2165114	SO:0000498	SO:0000299	five_prime_D_spacer	SO:0000669
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]	SO	1640214	SO:0000499	SO:0000001	virtual_sequence	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]	SO	1640215	SO:0000500	SO:0000001	Hoogsteen_base_pair	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A type of non-canonical base-pairing." [SO:ke]	SO	1640216	SO:0000501	SO:0000001	reverse_Hoogsteen_base_pair	SO:0000110
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640217	SO:0000504	SO:0000299	D_DJ_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640218	SO:0000505	SO:0000299	D_DJ_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640219	SO:0000506	SO:0000299	D_DJ_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640220	SO:0000508	SO:0000299	D_DJ_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640221	SO:0000509	SO:0000299	D_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640222	SO:0000510	SO:0000299	VD_gene_segment	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640223	SO:0000511	SO:0000299	J_C_cluster	SO:0000669
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	1640224	SO:0000512	SO:0000240	inversion_derived_deficiency_plus_aneuploid	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	1640225	SO:0000512	SO:0000240	inversion_derived_deficiency_plus_aneuploid	SO:0001524
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640226	SO:0000513	SO:0000299	J_cluster	SO:0000669
5	"" []	\N	specific_recombination_site	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640227	SO:0000514	SO:0000300	J_nonamer	SO:0000299
5	"" []	\N	specific_recombination_site	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640228	SO:0000515	SO:0000300	J_heptamer	SO:0000299
6	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1805625	SO:0000517	SO:0000299	J_spacer	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640230	SO:0000518	SO:0000299	V_DJ_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640231	SO:0000519	SO:0000299	V_DJ_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640232	SO:0000520	SO:0000299	V_VDJ_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640233	SO:0000521	SO:0000299	V_VDJ_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640234	SO:0000522	SO:0000299	V_VDJ_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640235	SO:0000523	SO:0000299	V_VJ_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640236	SO:0000524	SO:0000299	V_VJ_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640237	SO:0000525	SO:0000299	V_VJ_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640238	SO:0000526	SO:0000299	V_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640239	SO:0000527	SO:0000299	V_D_DJ_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640240	SO:0000528	SO:0000299	V_D_DJ_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640241	SO:0000529	SO:0000299	V_D_DJ_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640242	SO:0000530	SO:0000299	V_D_DJ_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640243	SO:0000531	SO:0000299	V_D_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640244	SO:0000532	SO:0000299	V_D_J_cluster	SO:0000669
5	"" []	\N	specific_recombination_site	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640245	SO:0000533	SO:0000300	V_heptamer	SO:0000299
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640246	SO:0000534	SO:0000299	V_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640247	SO:0000535	SO:0000299	V_J_C_cluster	SO:0000669
5	"" []	\N	specific_recombination_site	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640248	SO:0000536	SO:0000300	V_nonamer	SO:0000299
6	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1805626	SO:0000537	SO:0000299	V_spacer	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640250	SO:0000538	SO:0000299	V_gene_recombination_feature	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640251	SO:0000539	SO:0000299	DJ_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640252	SO:0000540	SO:0000299	DJ_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640253	SO:0000541	SO:0000299	VDJ_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640254	SO:0000542	SO:0000299	V_DJ_C_cluster	SO:0000669
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	1640255	SO:0000544	SO:0001037	helitron	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	1640256	SO:0000544	SO:0001037	helitron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	2731403	SO:0000545	SO:0000001	recoding_pseudoknot	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	1640258	SO:0000545	SO:0000233	recoding_pseudoknot	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	1640259	SO:0000545	SO:0000833	recoding_pseudoknot	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	1640260	SO:0000545	SO:0000833	recoding_pseudoknot	SO:0001411
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	1640261	SO:0000547	SO:0000240	inversion_derived_bipartite_duplication	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	1640262	SO:0000547	SO:0000240	inversion_derived_bipartite_duplication	SO:0001524
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes a transcript that is edited." [SO:xp]	SO	1640263	SO:0000548	SO:0000001	gene_with_edited_transcript	SO:0000110
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	1640264	SO:0000549	SO:0000240	inversion_derived_duplication_plus_aneuploid	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	1640265	SO:0000549	SO:0000240	inversion_derived_duplication_plus_aneuploid	SO:0001524
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	1640266	SO:0000550	SO:0001506	aneuploid_chromosome	SO:0001026
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640267	SO:0000551	SO:0001411	polyA_signal_sequence	SO:0000001
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	2165116	SO:0000552	SO:0000233	Shine_Dalgarno_sequence	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	2165117	SO:0000552	SO:0000833	Shine_Dalgarno_sequence	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	2165118	SO:0000552	SO:0000833	Shine_Dalgarno_sequence	SO:0001411
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	SOFA	mature_transcript	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640273	SO:0000553	SO:0000234	polyA_site	SO:0000233
5	"A region of a transcript." [SO:ke]	SOFA	transcript_region	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640274	SO:0000553	SO:0000834	polyA_site	SO:0000833
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2731404	SO:0000553	SO:0001411	polyA_site	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640276	SO:0000555	SO:0000673	five_prime_clip	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441307	SO:0000555	SO:0001411	five_prime_clip	SO:0000001
5	"" []	\N	specific_recombination_site	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640278	SO:0000556	SO:0000300	five_prime_D_recombination_signal_sequence	SO:0000299
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1640279	SO:0000557	SO:0000673	three_prime_clip	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441309	SO:0000557	SO:0001411	three_prime_clip	SO:0000001
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640281	SO:0000558	SO:0000299	C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640282	SO:0000559	SO:0000299	D_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640283	SO:0000560	SO:0000299	D_J_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640284	SO:0000561	SO:0000299	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"" []	SO	1640285	SO:0000562	SO:0000299	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000669
5	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	1640286	SO:0000563	SO:0000669	vertebrate_immune_system_gene_recombination_spacer	SO:0000298
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640287	SO:0000564	SO:0000299	V_DJ_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640288	SO:0000565	SO:0000299	V_VDJ_J_C_cluster	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640289	SO:0000566	SO:0000299	V_VJ_J_C_cluster	SO:0000669
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	1640290	SO:0000567	SO:0001507	inversion_derived_aneuploid_chromosome	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	1640291	SO:0000567	SO:0001524	inversion_derived_aneuploid_chromosome	SO:0001506
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1640292	SO:0000568	SO:0005836	bidirectional_promoter	SO:0000831
5	"" []	\N	specific_recombination_site	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640293	SO:0000570	SO:0000300	three_prime_D_recombination_signal_sequence	SO:0000299
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640294	SO:0000572	SO:0000299	DJ_gene_segment	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640295	SO:0000574	SO:0000299	VDJ_gene_segment	SO:0000669
5	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	1640296	SO:0000576	SO:0000299	VJ_gene_segment	SO:0000669
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	1640297	SO:0000577	SO:0001235	centromere	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]	SO	2165119	SO:0000577	SO:0000001	centromere	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	1640300	SO:0000580	SO:0000673	methylation_guide_snoRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	1640301	SO:0000582	SO:0000673	rRNA_cleavage_snoRNA_primary_transcript	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	1640302	SO:0000583	SO:0000831	pre_edited_region	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	2165120	SO:0000583	SO:0000001	pre_edited_region	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	1640304	SO:0000584	SO:0000673	tmRNA	SO:0000831
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1640305	SO:0000585	SO:0000733	C_D_box_snoRNA_encoding	SO:0000400
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	SO	1640306	SO:0000586	SO:0000831	tmRNA_primary_transcript	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	1640307	SO:0000587	SO:0000185	group_I_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	1640308	SO:0000587	SO:0000833	group_I_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	1640309	SO:0000587	SO:0000833	group_I_intron	SO:0001411
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	1640310	SO:0000588	SO:0000673	autocatalytically_spliced_intron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	2441331	SO:0000588	SO:0001411	autocatalytically_spliced_intron	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	SO	1640312	SO:0000589	SO:0000831	SRP_RNA_primary_transcript	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SO	1640313	SO:0000590	SO:0000831	SRP_RNA	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]	SO	1640314	SO:0000592	SO:0000001	H_pseudoknot	SO:0000110
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	1640315	SO:0000593	SO:0000673	C_D_box_snoRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	1640316	SO:0000594	SO:0000673	H_ACA_box_snoRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	1640317	SO:0000595	SO:0000673	C_D_box_snoRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	1640318	SO:0000596	SO:0000673	H_ACA_box_snoRNA_primary_transcript	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SO	1640319	SO:0000602	SO:0000831	guide_RNA	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	1640320	SO:0000603	SO:0000185	group_II_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	1640321	SO:0000603	SO:0000833	group_II_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	1640322	SO:0000603	SO:0000833	group_II_intron	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	1640323	SO:0000604	SO:0000831	editing_block	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	2165121	SO:0000604	SO:0000001	editing_block	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	1640325	SO:0000606	SO:0000831	editing_domain	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	2165122	SO:0000606	SO:0000001	editing_domain	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	1640327	SO:0000607	SO:0000831	unedited_region	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]	SO	2165123	SO:0000607	SO:0000001	unedited_region	SO:0000110
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1640329	SO:0000608	SO:0000733	H_ACA_box_snoRNA_encoding	SO:0000400
7	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	2165124	SO:0000611	SO:0000673	branch_site	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	2806625	SO:0000611	SO:0001411	branch_site	SO:0000001
7	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	2165126	SO:0000612	SO:0000673	polypyrimidine_tract	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	2806626	SO:0000612	SO:0001411	polypyrimidine_tract	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	2165128	SO:0000613	SO:0000831	bacterial_RNApol_promoter	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	1805627	SO:0000614	SO:0001411	bacterial_terminator	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	2081368	SO:0000615	SO:0000831	terminator_of_type_2_RNApol_III_promoter	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	1640343	SO:0000615	SO:0005836	terminator_of_type_2_RNApol_III_promoter	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	1640344	SO:0000616	SO:0000831	transcription_end_site	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The base where transcription ends." [SO:ke]	SO	2165129	SO:0000616	SO:0000001	transcription_end_site	SO:0000110
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1640346	SO:0000617	SO:0001055	RNApol_III_promoter_type_1	SO:0001679
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1640347	SO:0000618	SO:0001055	RNApol_III_promoter_type_2	SO:0001679
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	1640348	SO:0000619	SO:0000714	A_box	SO:0001683
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	1640349	SO:0000620	SO:0000714	B_box	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	1640350	SO:0000620	SO:0000167	B_box	SO:0001055
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1640351	SO:0000621	SO:0001055	RNApol_III_promoter_type_3	SO:0001679
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	1640352	SO:0000622	SO:0000714	C_box	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	1640353	SO:0000622	SO:0000167	C_box	SO:0001055
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	1640354	SO:0000624	SO:0001235	telomere	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]	SO	2165130	SO:0000624	SO:0000001	telomere	SO:0000110
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	1640356	SO:0000625	SO:0005836	silencer	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SO	1640358	SO:0000627	SO:0000831	insulator	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2165131	SO:0000629	SO:0000673	five_prime_open_reading_frame	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2806628	SO:0000629	SO:0001411	five_prime_open_reading_frame	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	1640362	SO:0000630	SO:0000233	upstream_AUG_codon	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	1640363	SO:0000630	SO:0000833	upstream_AUG_codon	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	1640364	SO:0000630	SO:0000833	upstream_AUG_codon	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	1640365	SO:0000631	SO:0001411	polycistronic_primary_transcript	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	1640366	SO:0000632	SO:0001411	monocistronic_primary_transcript	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	1805628	SO:0000633	SO:0001411	monocistronic_mRNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	1805629	SO:0000634	SO:0001411	polycistronic_mRNA	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	SO	1640369	SO:0000635	SO:0001411	mini_exon_donor_RNA	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640370	SO:0000636	SO:0000831	spliced_leader_RNA	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2165133	SO:0000636	SO:0000001	spliced_leader_RNA	SO:0000110
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	1805630	SO:0000638	SO:0000673	transcribed_spacer_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	2625347	SO:0000638	SO:0001411	transcribed_spacer_region	SO:0000001
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	1640376	SO:0000639	SO:0000483	internal_transcribed_spacer_region	SO:0000185
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	2081393	SO:0000639	SO:0000185	internal_transcribed_spacer_region	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	1640378	SO:0000639	SO:0000833	internal_transcribed_spacer_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	1640379	SO:0000639	SO:0000833	internal_transcribed_spacer_region	SO:0001411
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	1640380	SO:0000640	SO:0000483	external_transcribed_spacer_region	SO:0000185
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	2081396	SO:0000640	SO:0000185	external_transcribed_spacer_region	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	1640382	SO:0000640	SO:0000833	external_transcribed_spacer_region	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	1640383	SO:0000640	SO:0000833	external_transcribed_spacer_region	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640384	SO:0000641	SO:0000657	tetranucleotide_repeat_microsatellite_feature	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]	SO	1640385	SO:0000643	SO:0001411	minisatellite	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SO	1640386	SO:0000644	SO:0000831	antisense_RNA	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The reverse complement of the primary transcript." [SO:ke]	SO	1640387	SO:0000645	SO:0001411	antisense_primary_transcript	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SO	1640388	SO:0000646	SO:0000831	siRNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a micro RNA." [SO:ke]	SO	1640389	SO:0000647	SO:0000831	miRNA_primary_transcript	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	1640390	SO:0000648	SO:0000673	stRNA_primary_transcript	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SO	1640391	SO:0000649	SO:0000831	stRNA	SO:0001411
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	1640392	SO:0000650	SO:0000673	small_subunit_rRNA	SO:0000831
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	1640393	SO:0000651	SO:0000673	large_subunit_rRNA	SO:0000831
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	1640394	SO:0000652	SO:0000233	rRNA_5S	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	1640395	SO:0000653	SO:0000233	rRNA_28S	SO:0000673
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A mitochondrial gene located in a maxicircle." [SO:xp]	SO	1805631	SO:0000654	SO:0000001	maxicircle_gene	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SO	1640398	SO:0000655	SO:0001411	ncRNA	SO:0000001
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	1640399	SO:0000662	SO:0000673	spliceosomal_intron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	2441370	SO:0000662	SO:0001411	spliceosomal_intron	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is monocistronic." [SO:xp]	SO	1640402	SO:0000665	SO:0000001	monocistronic_transcript	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	1640403	SO:0000666	SO:0000673	mobile_intron	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A match against an EST sequence." [SO:ke]	SO	1640405	SO:0000668	SO:0001410	EST_match	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]	SO	1640406	SO:0000670	SO:0000001	chromosome_breakage_sequence	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]	SO	1640407	SO:0000671	SO:0000001	internal_eliminated_sequence	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]	SO	1640408	SO:0000672	SO:0000001	macronucleus_destined_segment	SO:0000110
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	1640409	SO:0000676	SO:0000835	canonical_three_prime_splice_site	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	1640410	SO:0000676	SO:0000835	canonical_three_prime_splice_site	SO:0000833
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	1640411	SO:0000677	SO:0000835	canonical_five_prime_splice_site	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	1640412	SO:0000677	SO:0000835	canonical_five_prime_splice_site	SO:0000833
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	1640413	SO:0000678	SO:0000835	non_canonical_three_prime_splice_site	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	1640414	SO:0000678	SO:0000835	non_canonical_three_prime_splice_site	SO:0000833
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	1640415	SO:0000679	SO:0000835	non_canonical_five_prime_splice_site	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	1640416	SO:0000679	SO:0000835	non_canonical_five_prime_splice_site	SO:0000833
5	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	1640417	SO:0000680	SO:0000316	non_canonical_start_codon	SO:0000836
6	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2081428	SO:0000680	SO:0000836	non_canonical_start_codon	SO:0000234
6	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2081429	SO:0000680	SO:0000836	non_canonical_start_codon	SO:0000834
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons." [SO:ke]	SO	1640420	SO:0000681	SO:0000001	aberrant_processed_transcript	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	1640421	SO:0000683	SO:0005836	exonic_splice_enhancer	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SO	1640422	SO:0000684	SO:0000409	nuclease_sensitive_site	SO:0001411
5	"A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]	\N	protein_binding_site	SOFA	SOFA	sequence	"" []	SO	1640423	SO:0000685	SO:0001654	DNAseI_hypersensitive_site	SO:0000410
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	1640424	SO:0000686	SO:0000240	translocation_element	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	1640425	SO:0000686	SO:0000240	translocation_element	SO:0001524
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]	SO	1640426	SO:0000688	SO:0000001	golden_path	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A match against cDNA sequence." [SO:ke]	SO	1640427	SO:0000689	SO:0001410	cDNA_match	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]	SO	2165134	SO:0000691	SO:0000001	cleaved_initiator_methionine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes a dicistronic transcript." [SO:xp]	SO	1640429	SO:0000692	SO:0000001	gene_with_dicistronic_transcript	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes an mRNA that is recoded." [SO:xp]	SO	1640430	SO:0000693	SO:0000001	gene_with_recoded_mRNA	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]	SO	1640431	SO:0000694	SO:0000001	SNP	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	SO	1640432	SO:0000697	SO:0001411	gene_with_stop_codon_read_through	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	1805634	SO:0000698	SO:0001411	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of sequence where the validity of the base calling is questionable." [SO:ke]	SO	1640434	SO:0000701	SO:0000001	possible_base_call_error	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of sequence where there may have been an error in the assembly." [SO:ke]	SO	1640435	SO:0000702	SO:0000001	possible_assembly_error	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	1640436	SO:0000706	SO:0000185	trans_splice_acceptor_site	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	1640437	SO:0000706	SO:0000833	trans_splice_acceptor_site	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	1640438	SO:0000706	SO:0000833	trans_splice_acceptor_site	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	1640439	SO:0000707	SO:0000185	trans_splice_donor_site	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	1640440	SO:0000707	SO:0000833	trans_splice_donor_site	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	1640441	SO:0000707	SO:0000833	trans_splice_donor_site	SO:0001411
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	1640442	SO:0000708	SO:0000835	SL1_acceptor_site	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	1640443	SO:0000708	SO:0000835	SL1_acceptor_site	SO:0000833
5	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1640444	SO:0000709	SO:0000835	SL2_acceptor_site	SO:0000185
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1640445	SO:0000709	SO:0000835	SL2_acceptor_site	SO:0000833
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	SO	1640446	SO:0000710	SO:0000704	gene_with_stop_codon_redefined_as_selenocysteine	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene with mRNA recoded by translational bypass." [SO:xp]	SO	1805635	SO:0000711	SO:0000001	gene_with_mRNA_recoded_by_translational_bypass	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene encoding a transcript that has a translational frameshift." [SO:xp]	SO	1640448	SO:0000712	SO:0001411	gene_with_transcript_with_translational_frameshift	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A motif that is active in the DNA form of the sequence." [SO:ke]	SO	1640449	SO:0000713	SO:0000001	DNA_motif	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A motif that is active in RNA sequence." [SO:ke]	SO	1640450	SO:0000715	SO:0000001	RNA_motif	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	2165135	SO:0000716	SO:0001411	dicistronic_mRNA	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SO	1640452	SO:0000719	SO:0001410	ultracontig	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transposable element that is foreign." [SO:ke]	SO	2081454	SO:0000720	SO:0000001	foreign_transposable_element	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable element that is foreign." [SO:ke]	SO	1640454	SO:0000720	SO:0001411	foreign_transposable_element	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes a dicistronic primary transcript." [SO:xp]	SO	1640455	SO:0000721	SO:0001411	gene_with_dicistronic_primary_transcript	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that encodes a polycistronic mRNA." [SO:xp]	SO	1640456	SO:0000722	SO:0001411	gene_with_dicistronic_mRNA	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens,SOFA	sequence_feature	SOFA	SOFA	sequence	"The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1805637	SO:0000725	SO:0000001	transit_peptide	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SO	1640459	SO:0000727	SO:0000831	CRM	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]	SO	2165136	SO:0000728	SO:0000001	intein	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	1640461	SO:0000734	SO:0000831	exemplar_mRNA	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"" []	SO	1640462	SO:0000752	SO:0001411	gene_group_regulatory_region	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	1640463	SO:0000754	SO:0001409	lambda_vector	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]	SO	2081460	SO:0000754	SO:0000001	lambda_vector	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1640465	SO:0000755	SO:0001409	plasmid_vector	SO:0000001
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1640466	SO:0000757	SO:0000443	single_stranded_cDNA	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1640467	SO:0000758	SO:0000443	double_stranded_cDNA	SO:0000400
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	1640468	SO:0000766	SO:0000673	pyrrolysyl_tRNA	SO:0000831
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A plasmid that may integrate with a chromosome." [SO:ma]	SO	1640469	SO:0000768	SO:0000001	episome	SO:0000110
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	1640470	SO:0000769	SO:0000655	tmRNA_coding_piece	SO:0000233
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	2441399	SO:0000769	SO:0000673	tmRNA_coding_piece	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	2806634	SO:0000769	SO:0001411	tmRNA_coding_piece	SO:0000001
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	1640473	SO:0000770	SO:0000655	tmRNA_acceptor_piece	SO:0000233
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	2441401	SO:0000770	SO:0000673	tmRNA_acceptor_piece	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	2806635	SO:0000770	SO:0001411	tmRNA_acceptor_piece	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	SO	2081469	SO:0000773	SO:0000001	pathogenic_island	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]	SO	1640478	SO:0000773	SO:0001411	pathogenic_island	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	2081470	SO:0000774	SO:0000001	metabolic_island	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	1640480	SO:0000774	SO:0001411	metabolic_island	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	SO	2081471	SO:0000775	SO:0000001	adaptive_island	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]	SO	1640482	SO:0000775	SO:0001411	adaptive_island	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	2081472	SO:0000776	SO:0000001	symbiosis_island	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]	SO	1640484	SO:0000776	SO:0001411	symbiosis_island	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An episome that is engineered." [SO:xp]	SO	1640485	SO:0000779	SO:0001411	engineered_episome	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A mini_gene that rescues." [SO:xp]	SO	1640487	SO:0000795	SO:0001410	rescue_mini_gene	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	SO	2081475	SO:0000796	SO:0000001	transgenic_transposable_element	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]	SO	1640489	SO:0000796	SO:0001411	transgenic_transposable_element	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"TE that has been modified by manipulations in vitro." [FB:mc]	SO	1640491	SO:0000798	SO:0001411	engineered_transposable_element	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable_element that is engineered and foreign." [FB:mc]	SO	1805642	SO:0000799	SO:0001411	engineered_foreign_transposable_element	SO:0000001
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	1640494	SO:0000800	SO:0001506	assortment_derived_duplication	SO:0001026
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	1640495	SO:0000801	SO:0001506	assortment_derived_deficiency_plus_duplication	SO:0001026
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	1640496	SO:0000802	SO:0001506	assortment_derived_deficiency	SO:0001026
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	1640497	SO:0000803	SO:0001506	assortment_derived_aneuploid	SO:0001026
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cDNA clone that has been validated." [SO:xp]	SO	1640499	SO:0000808	SO:0001409	validated_cDNA_clone	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cDNA clone that is invalid." [SO:xp]	SO	1640500	SO:0000809	SO:0001409	invalidated_cDNA_clone	SO:0000001
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A cDNA clone invalidated because it is chimeric." [SO:xp]	SO	1640501	SO:0000810	SO:0000695	chimeric_cDNA_clone	SO:0001409
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A cDNA clone invalidated by genomic contamination." [SO:xp]	SO	1640502	SO:0000811	SO:0000695	genomically_contaminated_cDNA_clone	SO:0001409
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A cDNA clone invalidated by polyA priming." [SO:xp]	SO	1640503	SO:0000812	SO:0000695	polyA_primed_cDNA_clone	SO:0001409
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A cDNA invalidated clone by partial processing." [SO:xp]	SO	1640504	SO:0000813	SO:0000695	partially_processed_cDNA_clone	SO:0001409
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]	SO	1640505	SO:0000815	SO:0000001	mini_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in a mitochondria." [SO:xp]	SO	1640506	SO:0000819	SO:0000001	mitochondrial_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in a chloroplast." [SO:xp]	SO	1640507	SO:0000820	SO:0000001	chloroplast_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in a chromoplast." [SO:xp]	SO	1640508	SO:0000821	SO:0000001	chromoplast_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in a cyanelle." [SO:xp]	SO	1640509	SO:0000822	SO:0000001	cyanelle_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome with origin in a leucoplast." [SO:xp]	SO	1640510	SO:0000823	SO:0000001	leucoplast_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in a macronucleus." [SO:xp]	SO	1640511	SO:0000824	SO:0000001	macronuclear_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in a micronucleus." [SO:xp]	SO	1640512	SO:0000825	SO:0000001	micronuclear_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in a nucleus." [SO:xp]	SO	1640513	SO:0000828	SO:0000001	nuclear_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in a nucleomorph." [SO:xp]	SO	1640514	SO:0000829	SO:0000001	nucleomorphic_chromosome	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	1640517	SO:0000836	SO:0000831	mRNA_region	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of an mRNA." [SO:cb]	SO	2165137	SO:0000836	SO:0000001	mRNA_region	SO:0000110
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	1640519	SO:0000837	SO:0000673	UTR_region	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	2441407	SO:0000837	SO:0001411	UTR_region	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	1805643	SO:0000838	SO:0000831	rRNA_primary_transcript_region	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of an rRNA primary transcript." [SO:ke]	SO	2486346	SO:0000838	SO:0000001	rRNA_primary_transcript_region	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	2165139	SO:0000841	SO:0000831	spliceosomal_intron_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region within an intron." [SO:ke]	SO	2731405	SO:0000841	SO:0000001	spliceosomal_intron_region	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	2165141	SO:0000847	SO:0000831	tmRNA_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	2731406	SO:0000847	SO:0000001	tmRNA_region	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a tmRNA." [SO:cb]	SO	1640527	SO:0000847	SO:0000233	tmRNA_region	SO:0000673
5	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	1640528	SO:0000848	SO:0000101	LTR_component	SO:0001039
5	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1640530	SO:0000849	SO:0000180	three_prime_LTR_component	SO:0000101
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885726	SO:0000849	SO:0001411	three_prime_LTR_component	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2917083	SO:0000849	SO:0000001	three_prime_LTR_component	SO:0000110
5	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	1640533	SO:0000850	SO:0000180	five_prime_LTR_component	SO:0000101
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885728	SO:0000850	SO:0001411	five_prime_LTR_component	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2917084	SO:0000850	SO:0000001	five_prime_LTR_component	SO:0000110
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	1805644	SO:0000851	SO:0000673	CDS_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	2625353	SO:0000851	SO:0001411	CDS_region	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A homologous_region that is paralogous to another region." [SO:ke]	SO	1640539	SO:0000854	SO:0000001	paralogous_region	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A homologous_region that is orthologous to another region." [SO:ke]	SO	1640540	SO:0000855	SO:0000001	orthologous_region	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript that is capped." [SO:xp]	SO	1640541	SO:0000861	SO:0001411	capped_primary_transcript	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA that is capped." [SO:xp]	SO	1640542	SO:0000862	SO:0000831	capped_mRNA	SO:0001411
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A frameshift caused by deleting one base." [SO:ke]	SO	1640543	SO:0000866	SO:0000733	minus_1_frameshift	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A frameshift caused by deleting two bases." [SO:ke]	SO	1640544	SO:0000867	SO:0000733	minus_2_frameshift	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A frameshift caused by inserting one base." [SO:ke]	SO	1640545	SO:0000868	SO:0000733	plus_1_frameshift	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A frameshift caused by inserting two bases." [SO:ke]	SO	1640546	SO:0000869	SO:0000733	plus_2_framshift	SO:0000400
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA that is polyadenylated." [SO:xp]	SO	1640547	SO:0000871	SO:0000831	polyadenylated_mRNA	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	1805647	SO:0000872	SO:0001411	trans_spliced_mRNA	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is edited." [SO:ke]	SO	1640549	SO:0000873	SO:0000001	edited_transcript	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that has been edited by A to I substitution." [SO:ke]	SO	1640550	SO:0000874	SO:0001411	edited_transcript_by_A_to_I_substitution	SO:0000001
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing the alteration of codon meaning." [SO:ke]	SO	1640551	SO:0000882	SO:0000733	codon_redefined	SO:0000400
5	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	1640552	SO:0000883	SO:0000316	stop_codon_read_through	SO:0000836
6	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2081505	SO:0000883	SO:0000836	stop_codon_read_through	SO:0000234
6	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2081506	SO:0000883	SO:0000836	stop_codon_read_through	SO:0000834
5	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	1640555	SO:0000884	SO:0000851	stop_codon_redefined_as_pyrrolysine	SO:0000316
5	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	1640556	SO:0000884	SO:0000851	stop_codon_redefined_as_pyrrolysine	SO:0000836
5	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	1640557	SO:0000885	SO:0000851	stop_codon_redefined_as_selenocysteine	SO:0000316
5	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	1640558	SO:0000885	SO:0000851	stop_codon_redefined_as_selenocysteine	SO:0000836
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Recoded mRNA where a block of nucleotides is not translated." [SO:ke]	SO	1640559	SO:0000886	SO:0000733	recoded_by_translational_bypass	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"Recoding by frameshifting a particular site." [SO:ke]	SO	1640560	SO:0000887	SO:0000733	translationally_frameshifted	SO:0000400
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	SO	1640561	SO:0000893	SO:0000401	silenced	SO:0000733
5	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	SO	1640562	SO:0000894	SO:0000119	silenced_by_DNA_modification	SO:0000401
5	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	1640563	SO:0000895	SO:0000123	silenced_by_DNA_methylation	SO:0000119
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is allelically_excluded." [SO:xp]	SO	1640564	SO:0000897	SO:0000001	allelically_excluded_gene	SO:0000110
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]	SO	1640565	SO:0000908	SO:0000733	supported_by_domain_match	SO:0000400
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]	SO	1640566	SO:0000909	SO:0000733	supported_by_EST_or_cDNA	SO:0000400
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640567	SO:0000912	SO:0000839	asx_turn	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640568	SO:0000912	SO:0000839	asx_turn	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A clone insert made from cDNA." [SO:xp]	SO	1805648	SO:0000913	SO:0000001	cloned_cDNA_insert	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A clone insert made from genomic DNA." [SO:xp]	SO	1805649	SO:0000914	SO:0000001	cloned_genomic_insert	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA that is edited." [SO:xp]	SO	1805650	SO:0000929	SO:0001411	edited_mRNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	1805651	SO:0000930	SO:0000831	guide_RNA_region	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of guide RNA." [SO:ma]	SO	2486347	SO:0000930	SO:0000001	guide_RNA_region	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	1640575	SO:0000931	SO:0000233	anchor_region	SO:0000673
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	2081522	SO:0000931	SO:0000673	anchor_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	2625362	SO:0000931	SO:0001411	anchor_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640578	SO:0000932	SO:0000831	pre_edited_mRNA	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]	SO	1640579	SO:0000934	SO:0000001	miRNA_target_site	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	1640580	SO:0000935	SO:0000233	edited_CDS	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	1640581	SO:0000935	SO:0000833	edited_CDS	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	1640582	SO:0000935	SO:0000833	edited_CDS	SO:0001411
5	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	1640583	SO:0000936	SO:0000669	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000298
5	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	1640584	SO:0000938	SO:0000669	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000298
5	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	1640585	SO:0000939	SO:0000669	vertebrate_immune_system_gene_recombination_signal_feature	SO:0000298
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]	SO	1640586	SO:0000941	SO:0000001	recombinationally_rearranged_vertebrate_immune_system_gene	SO:0000110
5	"" []	\N	recombination_feature	\N	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	1640587	SO:0000942	SO:0000669	attP_site	SO:0000298
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	1640588	SO:0000942	SO:0001037	attP_site	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	1640589	SO:0000942	SO:0001037	attP_site	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	2441437	SO:0000942	SO:0001411	attP_site	SO:0000001
5	"" []	\N	recombination_feature	\N	\N	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	1640591	SO:0000943	SO:0000669	attB_site	SO:0000298
5	"" []	\N	recombination_feature	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	1640592	SO:0000944	SO:0000669	attL_site	SO:0000298
5	"" []	\N	recombination_feature	\N	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	1640593	SO:0000945	SO:0000669	attR_site	SO:0000298
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	SO	1640594	SO:0000946	SO:0000298	integration_excision_site	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	SO	1640595	SO:0000947	SO:0000298	resolution_site	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	SO	1640596	SO:0000948	SO:0000298	inversion_site	SO:0001411
5	"" []	\N	recombination_feature	\N	\N	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	1640597	SO:0000949	SO:0000669	dif_site	SO:0000298
5	"" []	\N	recombination_feature	\N	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	1640598	SO:0000950	SO:0000669	attC_site	SO:0000298
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	2548811	SO:0000950	SO:0000001	attC_site	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	2441445	SO:0000950	SO:0001411	attC_site	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1805652	SO:0000951	SO:0001411	eukaryotic_terminator	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, DNA molecule." [SO:ma]	SO	1640603	SO:0000954	SO:0000001	DNA_chromosome	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	SO	1640604	SO:0000955	SO:0001411	double_stranded_DNA_chromosome	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	SO	1640605	SO:0000956	SO:0001411	single_stranded_DNA_chromosome	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	SO	1640606	SO:0000957	SO:0001235	linear_double_stranded_DNA_chromosome	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	SO	1640607	SO:0000958	SO:0001235	circular_double_stranded_DNA_chromosome	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	SO	1640608	SO:0000959	SO:0001235	linear_single_stranded_DNA_chromosome	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	1640609	SO:0000960	SO:0001235	circular_single_stranded_DNA_chromosome	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, RNA molecule." [SO:ma]	SO	1640610	SO:0000961	SO:0000001	RNA_chromosome	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	SO	1640611	SO:0000962	SO:0001411	single_stranded_RNA_chromosome	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	SO	1640612	SO:0000963	SO:0001235	linear_single_stranded_RNA_chromosome	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	SO	1640613	SO:0000964	SO:0001235	linear_double_stranded_RNA_chromosome	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	SO	1640614	SO:0000965	SO:0001411	double_stranded_RNA_chromosome	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	1640615	SO:0000966	SO:0001235	circular_single_stranded_RNA_chromosome	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	SO	1640616	SO:0000967	SO:0001235	circular_double_stranded_RNA_chromosome	SO:0001411
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	1640617	SO:0000973	SO:0001039	insertion_sequence	SO:0001037
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1805653	SO:0000975	SO:0000001	minicircle_gene	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	1640621	SO:0000978	SO:0000233	template_region	SO:0000673
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	2081558	SO:0000978	SO:0000673	template_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	2625363	SO:0000978	SO:0001411	template_region	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081562	SO:0000981	SO:0000831	rho_dependent_bacterial_terminator	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1640625	SO:0000981	SO:0005836	rho_dependent_bacterial_terminator	SO:0000831
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081564	SO:0000982	SO:0000831	rho_independent_bacterial_terminator	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1640627	SO:0000982	SO:0005836	rho_independent_bacterial_terminator	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	1640628	SO:0000989	SO:0000831	class_II_RNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	1640629	SO:0000990	SO:0000831	class_I_RNA	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1805654	SO:0000992	SO:0001409	BAC_cloned_genomic_insert	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1640632	SO:0000995	SO:0000831	consensus_mRNA	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	1640633	SO:0000998	SO:0000185	recursive_splice_site	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	1640634	SO:0000998	SO:0000833	recursive_splice_site	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	1640635	SO:0000998	SO:0000833	recursive_splice_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	2899072	SO:0000999	SO:0000001	BAC_end	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	1640637	SO:0000999	SO:0000719	BAC_end	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	2081571	SO:0000999	SO:0001876	BAC_end	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	2486348	SO:0000999	SO:0001248	BAC_end	SO:0001410
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	1640640	SO:0000999	SO:0000695	BAC_end	SO:0001409
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	1640641	SO:0000999	SO:0001411	BAC_end	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	1640642	SO:0001000	SO:0000233	rRNA_16S	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	1640643	SO:0001001	SO:0000233	rRNA_23S	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	1640644	SO:0001002	SO:0000233	rRNA_25S	SO:0000673
5	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	1640645	SO:0001003	SO:0000101	solo_LTR	SO:0001039
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	2731409	SO:0001003	SO:0000001	solo_LTR	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	SO	2081579	SO:0001006	SO:0000001	prophage	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl]	SO	1640648	SO:0001006	SO:0001411	prophage	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	SO	2081580	SO:0001007	SO:0000001	cryptic_prophage	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl]	SO	1640650	SO:0001007	SO:0001411	cryptic_prophage	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]	SO	1640651	SO:0001008	SO:0001411	tetraloop	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	SO	1640652	SO:0001009	SO:0001409	DNA_constraint_sequence	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]	SO	1640653	SO:0001010	SO:0000001	i_motif	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]	SO	1640654	SO:0001011	SO:0001409	PNA_oligo	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequence with catalytic activity." [SO:cb]	SO	1640655	SO:0001012	SO:0000001	DNAzyme	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	SO	1640656	SO:0001013	SO:0000001	MNP	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1805656	SO:0001014	SO:0000831	intron_domain	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2486349	SO:0001014	SO:0000001	intron_domain	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]	SO	1640659	SO:0001015	SO:0000001	wobble_base_pair	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	2165147	SO:0001016	SO:0000673	internal_guide_sequence	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	2806638	SO:0001016	SO:0001411	internal_guide_sequence	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640662	SO:0001021	SO:0000001	chromosome_breakpoint	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	1640663	SO:0001022	SO:0001411	inversion_breakpoint	SO:0000001
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1640664	SO:0001033	SO:0000735	chloroplast_DNA	SO:0000400
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	1805660	SO:0001034	SO:0000673	mirtron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	2625367	SO:0001034	SO:0001411	mirtron	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	SO	1640667	SO:0001035	SO:0000831	piRNA	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	1640668	SO:0001036	SO:0000673	arginyl_tRNA	SO:0000831
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The nucleotide sequence of a virus that infects bacteria." [SO:ke]	SO	1805662	SO:0001042	SO:0000001	phage_sequence	SO:0000110
5	"" []	\N	recombination_feature	\N	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	1640672	SO:0001043	SO:0000669	attCtn_site	SO:0000298
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	1640673	SO:0001043	SO:0001039	attCtn_site	SO:0001037
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]	SO	1640674	SO:0001044	SO:0000001	nuclear_mt_pseudogene	SO:0000110
5	"" []	\N	recombination_feature	\N	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	1640676	SO:0001046	SO:0000669	IRLinv_site	SO:0000298
5	"" []	\N	recombination_feature	\N	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	1640677	SO:0001047	SO:0000669	IRRinv_site	SO:0000298
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region located within an inversion site." [SO:ke]	SO	1640678	SO:0001048	SO:0000298	inversion_site_part	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	SO	2081598	SO:0001049	SO:0000001	defective_conjugative_transposon	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]	SO	1640680	SO:0001049	SO:0001411	defective_conjugative_transposon	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	1640682	SO:0001054	SO:0001037	transposon_fragment	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	1640683	SO:0001054	SO:0001037	transposon_fragment	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SO	1640684	SO:0001055	SO:0001411	transcriptional_cis_regulatory_region	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A regulatory_region that modulates splicing." [SO:ke]	SO	1640685	SO:0001056	SO:0001411	splicing_regulatory_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	SO	1640686	SO:0001058	SO:0000831	promoter_targeting_sequence	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]	SO	2486350	SO:0001061	SO:0000001	propeptide_cleavage_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]	SO	2165151	SO:0001062	SO:0000001	propeptide	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]	SO	2165152	SO:0001064	SO:0000001	active_peptide	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	SO	1805668	SO:0001067	SO:0000001	polypeptide_motif	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]	SO	1805669	SO:0001068	SO:0000001	polypeptide_repeat	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]	SO	1805670	SO:0001071	SO:0000001	membrane_structure	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]	SO	2165153	SO:0001072	SO:0000001	extramembrane_polypeptide_region	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	1805673	SO:0001073	SO:0000104	cytoplasmic_polypeptide_region	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	2279428	SO:0001073	SO:0001411	cytoplasmic_polypeptide_region	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	1805675	SO:0001074	SO:0000104	non_cytoplasmic_polypeptide_region	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	2279430	SO:0001074	SO:0001411	non_cytoplasmic_polypeptide_region	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Polypeptide region present in the lipid bilayer." [EBIBS:GAR]	SO	2165154	SO:0001075	SO:0000001	intramembrane_polypeptide_region	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	1805679	SO:0001076	SO:0000104	membrane_peptide_loop	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	2279432	SO:0001076	SO:0001411	membrane_peptide_loop	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	1805681	SO:0001077	SO:0000104	transmembrane_polypeptide_region	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	2279434	SO:0001077	SO:0001411	transmembrane_polypeptide_region	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	SO	1805683	SO:0001078	SO:0000001	polypeptide_secondary_structure	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]	SO	1805684	SO:0001079	SO:0000001	polypeptide_structural_motif	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	1640710	SO:0001080	SO:0000104	coiled_coil	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	2081608	SO:0001080	SO:0001411	coiled_coil	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	1640712	SO:0001081	SO:0000104	helix_turn_helix	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	2081610	SO:0001081	SO:0001411	helix_turn_helix	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]	SO	1640714	SO:0001083	SO:0000001	non_adjacent_residues	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]	SO	1640715	SO:0001084	SO:0000001	non_terminal_residue	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]	SO	1640716	SO:0001085	SO:0000001	sequence_conflict	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]	SO	1640717	SO:0001086	SO:0000001	sequence_uncertainty	SO:0000110
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	1640718	SO:0001089	SO:0000839	post_translationally_modified_region	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	1640719	SO:0001089	SO:0000839	post_translationally_modified_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	2731410	SO:0001092	SO:0000001	polypeptide_metal_contact	SO:0000110
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	1640721	SO:0001092	SO:0100021	polypeptide_metal_contact	SO:0000839
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	2731411	SO:0001093	SO:0000001	protein_protein_contact	SO:0000110
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	1640723	SO:0001093	SO:0100021	protein_protein_contact	SO:0000839
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	2885738	SO:0001094	SO:0001411	polypeptide_calcium_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	1640725	SO:0001094	SO:0001067	polypeptide_calcium_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	2885739	SO:0001095	SO:0001411	polypeptide_cobalt_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	1640727	SO:0001095	SO:0001067	polypeptide_cobalt_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	2885740	SO:0001096	SO:0001411	polypeptide_copper_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	1640729	SO:0001096	SO:0001067	polypeptide_copper_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	2885741	SO:0001097	SO:0001411	polypeptide_iron_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	1640731	SO:0001097	SO:0001067	polypeptide_iron_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	2885742	SO:0001098	SO:0001411	polypeptide_magnesium_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	1640733	SO:0001098	SO:0001067	polypeptide_magnesium_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	2885743	SO:0001099	SO:0001411	polypeptide_manganese_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	1640735	SO:0001099	SO:0001067	polypeptide_manganese_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	2885744	SO:0001100	SO:0001411	polypeptide_molybdenum_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	1640737	SO:0001100	SO:0001067	polypeptide_molybdenum_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	2885745	SO:0001101	SO:0001411	polypeptide_nickel_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	1640739	SO:0001101	SO:0001067	polypeptide_nickel_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	2885746	SO:0001102	SO:0001411	polypeptide_tungsten_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	1640741	SO:0001102	SO:0001067	polypeptide_tungsten_ion_contact_site	SO:0100021
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	2885747	SO:0001103	SO:0001411	polypeptide_zinc_ion_contact_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	biosapiens	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	1640743	SO:0001103	SO:0001067	polypeptide_zinc_ion_contact_site	SO:0100021
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	1640744	SO:0001104	SO:0100021	catalytic_residue	SO:0000839
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	2731412	SO:0001105	SO:0000001	polypeptide_ligand_contact	SO:0000110
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	1640746	SO:0001105	SO:0100021	polypeptide_ligand_contact	SO:0000839
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640747	SO:0001106	SO:0000104	asx_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081642	SO:0001106	SO:0001411	asx_motif	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640749	SO:0001107	SO:0000104	beta_bulge	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081644	SO:0001107	SO:0001411	beta_bulge	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640751	SO:0001108	SO:0000104	beta_bulge_loop	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081646	SO:0001108	SO:0001411	beta_bulge_loop	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640753	SO:0001109	SO:0000839	beta_bulge_loop_five	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640754	SO:0001109	SO:0000839	beta_bulge_loop_five	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640755	SO:0001110	SO:0000839	beta_bulge_loop_six	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640756	SO:0001110	SO:0000839	beta_bulge_loop_six	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	1640757	SO:0001111	SO:0000104	beta_strand	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	2081652	SO:0001111	SO:0001411	beta_strand	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	1640759	SO:0001112	SO:0000839	antiparallel_beta_strand	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	1640760	SO:0001112	SO:0000839	antiparallel_beta_strand	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	1640761	SO:0001113	SO:0000839	parallel_beta_strand	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	1640762	SO:0001113	SO:0000839	parallel_beta_strand	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	1640763	SO:0001114	SO:0000104	peptide_helix	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	2081658	SO:0001114	SO:0001411	peptide_helix	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	1640765	SO:0001115	SO:0000839	left_handed_peptide_helix	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	1640766	SO:0001115	SO:0000839	left_handed_peptide_helix	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	1640767	SO:0001116	SO:0000839	right_handed_peptide_helix	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	1640768	SO:0001116	SO:0000839	right_handed_peptide_helix	SO:0001411
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	1640769	SO:0001117	SO:0001070	alpha_helix	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	1640770	SO:0001118	SO:0001070	pi_helix	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	1640771	SO:0001119	SO:0001070	three_ten_helix	SO:0000839
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640772	SO:0001120	SO:0000104	polypeptide_nest_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081670	SO:0001120	SO:0001411	polypeptide_nest_motif	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640774	SO:0001121	SO:0000839	polypeptide_nest_left_right_motif	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640775	SO:0001121	SO:0000839	polypeptide_nest_left_right_motif	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640776	SO:0001122	SO:0000839	polypeptide_nest_right_left_motif	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640777	SO:0001122	SO:0000839	polypeptide_nest_right_left_motif	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640778	SO:0001123	SO:0000104	schellmann_loop	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081676	SO:0001123	SO:0001411	schellmann_loop	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640780	SO:0001124	SO:0000839	schellmann_loop_seven	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640781	SO:0001124	SO:0000839	schellmann_loop_seven	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640782	SO:0001125	SO:0000839	schellmann_loop_six	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640783	SO:0001125	SO:0000839	schellmann_loop_six	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640784	SO:0001126	SO:0000104	serine_threonine_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081682	SO:0001126	SO:0001411	serine_threonine_motif	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640786	SO:0001127	SO:0000104	serine_threonine_staple_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081684	SO:0001127	SO:0001411	serine_threonine_staple_motif	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	1640788	SO:0001128	SO:0000104	polypeptide_turn_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	2081686	SO:0001128	SO:0001411	polypeptide_turn_motif	SO:0000001
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640790	SO:0001129	SO:0001070	asx_turn_left_handed_type_one	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640791	SO:0001130	SO:0001070	asx_turn_left_handed_type_two	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640792	SO:0001131	SO:0001070	asx_turn_right_handed_type_two	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640793	SO:0001132	SO:0001070	asx_turn_right_handed_type_one	SO:0000839
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640794	SO:0001133	SO:0000839	beta_turn	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640795	SO:0001133	SO:0000839	beta_turn	SO:0001411
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640796	SO:0001134	SO:0001070	beta_turn_left_handed_type_one	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640797	SO:0001135	SO:0001070	beta_turn_left_handed_type_two	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640798	SO:0001136	SO:0001070	beta_turn_right_handed_type_one	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640799	SO:0001137	SO:0001070	beta_turn_right_handed_type_two	SO:0000839
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640800	SO:0001138	SO:0000839	gamma_turn	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640801	SO:0001138	SO:0000839	gamma_turn	SO:0001411
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640802	SO:0001139	SO:0001070	gamma_turn_classic	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640803	SO:0001140	SO:0001070	gamma_turn_inverse	SO:0000839
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640804	SO:0001141	SO:0000839	serine_threonine_turn	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640805	SO:0001141	SO:0000839	serine_threonine_turn	SO:0001411
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640806	SO:0001142	SO:0001070	st_turn_left_handed_type_one	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640807	SO:0001143	SO:0001070	st_turn_left_handed_type_two	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640808	SO:0001144	SO:0001070	st_turn_right_handed_type_one	SO:0000839
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1640809	SO:0001145	SO:0001070	st_turn_right_handed_type_two	SO:0000839
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]	SO	1805685	SO:0001147	SO:0000001	natural_variant_site	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]	SO	1805686	SO:0001148	SO:0000001	mutated_variant_site	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]	SO	1805687	SO:0001149	SO:0000001	alternate_sequence_site	SO:0000110
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	1640816	SO:0001150	SO:0001070	beta_turn_type_six	SO:0000839
5	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	1640817	SO:0001151	SO:0001078	beta_turn_type_six_a	SO:0001070
5	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"" []	SO	1640818	SO:0001152	SO:0001128	beta_turn_type_six_a_one	SO:0001078
5	"A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]	biosapiens	polypeptide_secondary_structure	biosapiens	biosapiens	sequence	"" []	SO	1640819	SO:0001153	SO:0001128	beta_turn_type_six_a_two	SO:0001078
5	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	1640820	SO:0001154	SO:0001078	beta_turn_type_six_b	SO:0001070
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	1640821	SO:0001155	SO:0001070	beta_turn_type_eight	SO:0000839
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	2885756	SO:0001156	SO:0001411	DRE_motif	SO:0000001
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	1640823	SO:0001156	SO:0001055	DRE_motif	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	SO	1640824	SO:0001157	SO:0001683	DMv4_motif	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	2885757	SO:0001158	SO:0001411	E_box_motif	SO:0000001
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	1640826	SO:0001158	SO:0001055	E_box_motif	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	1640827	SO:0001159	SO:0001683	DMv5_motif	SO:0001411
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	1640828	SO:0001159	SO:0001055	DMv5_motif	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	1640829	SO:0001160	SO:0001683	DMv3_motif	SO:0001411
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	1640830	SO:0001160	SO:0001055	DMv3_motif	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	1640831	SO:0001161	SO:0001683	DMv2_motif	SO:0001411
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	1640832	SO:0001161	SO:0001055	DMv2_motif	SO:0001679
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	1640833	SO:0001162	SO:0000714	MTE	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	1640834	SO:0001162	SO:0000167	MTE	SO:0001055
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	2885762	SO:0001163	SO:0001411	INR1_motif	SO:0000001
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	1640836	SO:0001163	SO:0001055	INR1_motif	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	1640837	SO:0001164	SO:0001683	DPE1_motif	SO:0001411
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	1640838	SO:0001164	SO:0001055	DPE1_motif	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	1640839	SO:0001165	SO:0001683	DMv1_motif	SO:0001411
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	1640840	SO:0001165	SO:0001055	DMv1_motif	SO:0001679
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	2885765	SO:0001166	SO:0001411	GAGA_motif	SO:0000001
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	1640842	SO:0001166	SO:0001055	GAGA_motif	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	1640843	SO:0001167	SO:0001683	NDM2_motif	SO:0001411
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	1640844	SO:0001167	SO:0001055	NDM2_motif	SO:0001679
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	1640845	SO:0001168	SO:0001683	NDM3_motif	SO:0001411
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	1640846	SO:0001168	SO:0001055	NDM3_motif	SO:0001679
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]	SO	1805688	SO:0001169	SO:0000001	ds_RNA_viral_sequence	SO:0000110
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	1640849	SO:0001170	SO:0001039	polinton	SO:0001037
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	1640850	SO:0001171	SO:0000233	rRNA_21S	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	1805689	SO:0001172	SO:0000831	tRNA_region	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a tRNA." [RSC:cb]	SO	2486354	SO:0001172	SO:0000001	tRNA_region	SO:0000110
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	1640854	SO:0001173	SO:0000233	anticodon_loop	SO:0000673
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	2081759	SO:0001173	SO:0000673	anticodon_loop	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	2625382	SO:0001173	SO:0001411	anticodon_loop	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	1805690	SO:0001174	SO:0000233	anticodon	SO:0000673
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	2279450	SO:0001174	SO:0000673	anticodon	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	2806639	SO:0001174	SO:0001411	anticodon	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	1640860	SO:0001175	SO:0000233	CCA_tail	SO:0000673
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	2081764	SO:0001175	SO:0000673	CCA_tail	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	2625384	SO:0001175	SO:0001411	CCA_tail	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	1640863	SO:0001176	SO:0000233	DHU_loop	SO:0000673
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	2081767	SO:0001176	SO:0000673	DHU_loop	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	2625385	SO:0001176	SO:0001411	DHU_loop	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	1640866	SO:0001177	SO:0000233	T_loop	SO:0000673
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	2081770	SO:0001177	SO:0000673	T_loop	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	2625386	SO:0001177	SO:0001411	T_loop	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	1640869	SO:0001178	SO:0000673	pyrrolysine_tRNA_primary_transcript	SO:0000831
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	1640870	SO:0001179	SO:0000233	U3_snoRNA	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	1805693	SO:0001180	SO:0000233	AU_rich_element	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	1805694	SO:0001180	SO:0000833	AU_rich_element	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	1805695	SO:0001180	SO:0000833	AU_rich_element	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	1805696	SO:0001181	SO:0000233	Bruno_response_element	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	1805697	SO:0001181	SO:0000833	Bruno_response_element	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	1805698	SO:0001181	SO:0000833	Bruno_response_element	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	1640877	SO:0001182	SO:0000233	iron_responsive_element	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	1640878	SO:0001182	SO:0000833	iron_responsive_element	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	1640879	SO:0001182	SO:0000833	iron_responsive_element	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	1640880	SO:0001187	SO:0000233	pseudouridylation_guide_snoRNA	SO:0000673
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An oligo composed of LNA residues." [RSC:cb]	SO	1640881	SO:0001189	SO:0001409	LNA_oligo	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An oligo composed of TNA residues." [RSC:cb]	SO	1640882	SO:0001191	SO:0001409	TNA_oligo	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An oligo composed of GNA residues." [RSC:cb]	SO	1640883	SO:0001193	SO:0001409	GNA_oligo	SO:0000001
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An oligo composed of (R)-GNA residues." [RSC:cb]	SO	1640884	SO:0001195	SO:0000695	R_GNA_oligo	SO:0001409
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An oligo composed of (S)-GNA residues." [RSC:cb]	SO	1640885	SO:0001197	SO:0000695	S_GNA_oligo	SO:0001409
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]	SO	1805699	SO:0001198	SO:0000001	ds_DNA_viral_sequence	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]	SO	1805700	SO:0001199	SO:0000001	ss_RNA_viral_sequence	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	1640890	SO:0001200	SO:0001037	negative_sense_ssRNA_viral_sequence	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	1640891	SO:0001200	SO:0001037	negative_sense_ssRNA_viral_sequence	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	2081788	SO:0001200	SO:0001411	negative_sense_ssRNA_viral_sequence	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	1640893	SO:0001201	SO:0001037	positive_sense_ssRNA_viral_sequence	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	1640894	SO:0001201	SO:0001037	positive_sense_ssRNA_viral_sequence	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	2081790	SO:0001201	SO:0001411	positive_sense_ssRNA_viral_sequence	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	1640896	SO:0001202	SO:0001037	ambisense_ssRNA_viral_sequence	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	1640897	SO:0001202	SO:0001037	ambisense_ssRNA_viral_sequence	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	2081792	SO:0001202	SO:0001411	ambisense_ssRNA_viral_sequence	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1640899	SO:0001203	SO:0005836	RNA_polymerase_promoter	SO:0000831
5	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1640900	SO:0001204	SO:0001679	Phage_RNA_Polymerase_Promoter	SO:0005836
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1640901	SO:0001205	SO:0001055	SP6_RNA_Polymerase_Promoter	SO:0001679
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1640902	SO:0001206	SO:0001055	T3_RNA_Polymerase_Promoter	SO:0001679
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	1640903	SO:0001207	SO:0001055	T7_RNA_Polymerase_Promoter	SO:0001679
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	1640904	SO:0001208	SO:0000695	five_prime_EST	SO:0001409
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	1640905	SO:0001209	SO:0000695	three_prime_EST	SO:0001409
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1640906	SO:0001210	SO:0000673	translational_frameshift	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2441626	SO:0001210	SO:0001411	translational_frameshift	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1640908	SO:0001211	SO:0000233	plus_1_translational_frameshift	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1640909	SO:0001211	SO:0000833	plus_1_translational_frameshift	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1640910	SO:0001211	SO:0000833	plus_1_translational_frameshift	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1640911	SO:0001212	SO:0000233	plus_2_translational_frameshift	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1640912	SO:0001212	SO:0000833	plus_2_translational_frameshift	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	1640913	SO:0001212	SO:0000833	plus_2_translational_frameshift	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	1640914	SO:0001213	SO:0000185	group_III_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	1640915	SO:0001213	SO:0000833	group_III_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	1640916	SO:0001213	SO:0000833	group_III_intron	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	1805701	SO:0001214	SO:0000831	noncoding_region_of_exon	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The maximal intersection of exon and UTR." [SO:ke]	SO	2486355	SO:0001214	SO:0000001	noncoding_region_of_exon	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	1805703	SO:0001215	SO:0000831	coding_region_of_exon	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The region of an exon that encodes for protein sequence." [SO:ke]	SO	2486356	SO:0001215	SO:0000001	coding_region_of_exon	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1640921	SO:0001216	SO:0000673	endonuclease_spliced_intron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	2441633	SO:0001216	SO:0001411	endonuclease_spliced_intron	SO:0000001
5	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	SO	1640923	SO:0001220	SO:0000119	silenced_by_RNA_interference	SO:0000401
5	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	SO	1640924	SO:0001221	SO:0000119	silenced_by_histone_modification	SO:0000401
5	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	1640925	SO:0001222	SO:0000123	silenced_by_histone_methylation	SO:0000119
5	"An attribute to describe a sequence that is regulated." [SO:ke]	\N	regulated	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	1640926	SO:0001223	SO:0000123	silenced_by_histone_deacetylation	SO:0000119
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is silenced by RNA interference." [SO:xp]	SO	1640927	SO:0001224	SO:0000001	gene_silenced_by_RNA_interference	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is silenced by histone modification." [SO:xp]	SO	1640928	SO:0001225	SO:0000001	gene_silenced_by_histone_modification	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is silenced by histone methylation." [SO:xp]	SO	1640929	SO:0001226	SO:0001411	gene_silenced_by_histone_methylation	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene that is silenced by histone deacetylation." [SO:xp]	SO	1640930	SO:0001227	SO:0001411	gene_silenced_by_histone_deacetylation	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]	SO	1640931	SO:0001228	SO:0001411	dihydrouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]	SO	1640932	SO:0001229	SO:0001411	pseudouridine	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]	SO	1640933	SO:0001230	SO:0000001	inosine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]	SO	1640934	SO:0001231	SO:0000001	seven_methylguanine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]	SO	1640935	SO:0001232	SO:0000001	ribothymidine	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	SO	1640936	SO:0001233	SO:0001236	methylinosine	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1640937	SO:0001238	SO:0000673	major_TSS	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441639	SO:0001238	SO:0001411	major_TSS	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	1640939	SO:0001239	SO:0000673	minor_TSS	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441640	SO:0001239	SO:0001411	minor_TSS	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	1640941	SO:0001243	SO:0000831	miRNA_primary_transcript_region	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A part of an miRNA primary_transcript." [SO:ke]	SO	2165158	SO:0001243	SO:0000001	miRNA_primary_transcript_region	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	1640943	SO:0001244	SO:0000673	pre_miRNA	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	2441641	SO:0001244	SO:0001411	pre_miRNA	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1805705	SO:0001245	SO:0000673	miRNA_stem	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	2625391	SO:0001245	SO:0001411	miRNA_stem	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	1805707	SO:0001246	SO:0000673	miRNA_loop	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	2625392	SO:0001246	SO:0001411	miRNA_loop	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An oligo composed of synthetic nucleotides." [SO:ke]	SO	1640949	SO:0001247	SO:0000001	synthetic_oligo	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]	SO	1640950	SO:0001250	SO:0000001	fingerprint_map	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An STS map is a physical map organized by the unique STS landmarks." [SO:ke]	SO	1640951	SO:0001251	SO:0000001	STS_map	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A radiation hybrid map is a physical map." [SO:ke]	SO	1640952	SO:0001252	SO:0000001	RH_map	SO:0000110
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	1640953	SO:0001254	SO:0001506	polyploid	SO:0001026
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	1640954	SO:0001255	SO:0001507	autopolyploid	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	1640955	SO:0001255	SO:0001524	autopolyploid	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	1640956	SO:0001256	SO:0001507	allopolyploid	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	1640957	SO:0001256	SO:0001524	allopolyploid	SO:0001506
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	SO	1640958	SO:0001257	SO:0000409	homing_endonuclease_binding_site	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	2885775	SO:0001258	SO:0001411	octamer_motif	SO:0000001
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	1640960	SO:0001258	SO:0001055	octamer_motif	SO:0001679
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A chromosome originating in an apicoplast." [SO:xp]	SO	1640961	SO:0001259	SO:0000001	apicoplast_chromosome	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]	SO	1640962	SO:0001261	SO:0000001	overlapping_feature_set	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]	SO	1640963	SO:0001262	SO:0001410	overlapping_EST_set	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640964	SO:0001264	SO:0000001	gRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640965	SO:0001265	SO:0000001	miRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640966	SO:0001266	SO:0000001	scRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640967	SO:0001267	SO:0000001	snoRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640968	SO:0001268	SO:0000001	snRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640969	SO:0001269	SO:0000001	SRP_RNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640970	SO:0001270	SO:0000001	stRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640971	SO:0001271	SO:0000001	tmRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640972	SO:0001272	SO:0000001	tRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified adenine is an adenine base feature that has been altered." [SO:ke]	SO	1640973	SO:0001273	SO:0000001	modified_adenosine	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	SO	1640974	SO:0001274	SO:0001411	modified_inosine	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified cytidine is a cytidine base feature which has been altered." [SO:ke]	SO	1640975	SO:0001275	SO:0000001	modified_cytidine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640976	SO:0001276	SO:0000001	modified_guanosine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1640977	SO:0001277	SO:0000001	modified_uridine	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	1640978	SO:0001278	SO:0001236	one_methylinosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	1640979	SO:0001279	SO:0001236	one_two_prime_O_dimethylinosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	1640980	SO:0001280	SO:0001236	two_prime_O_methylinosine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640981	SO:0001281	SO:0001411	three_methylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640982	SO:0001282	SO:0001411	five_methylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640983	SO:0001283	SO:0001411	two_prime_O_methylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640984	SO:0001284	SO:0001411	two_thiocytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640985	SO:0001285	SO:0001411	N4_acetylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640986	SO:0001286	SO:0001411	five_formylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640987	SO:0001287	SO:0001411	five_two_prime_O_dimethylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640988	SO:0001288	SO:0001411	N4_acetyl_2_prime_O_methylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640989	SO:0001289	SO:0001411	lysidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640990	SO:0001290	SO:0001411	N4_methylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640991	SO:0001291	SO:0001411	N4_2_prime_O_dimethylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640992	SO:0001292	SO:0001411	five_hydroxymethylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640993	SO:0001293	SO:0001411	five_formyl_two_prime_O_methylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	1640994	SO:0001294	SO:0001411	N4_N4_2_prime_O_trimethylcytidine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1640995	SO:0001295	SO:0001411	one_methyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1640996	SO:0001296	SO:0001411	two_methyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1640997	SO:0001297	SO:0001411	N6_methyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1640998	SO:0001298	SO:0001411	two_prime_O_methyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1640999	SO:0001299	SO:0001411	two_methylthio_N6_methyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641000	SO:0001300	SO:0001411	N6_isopentenyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641001	SO:0001301	SO:0001411	two_methylthio_N6_isopentenyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641002	SO:0001302	SO:0001411	N6_cis_hydroxyisopentenyl_adenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641003	SO:0001303	SO:0001411	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641004	SO:0001304	SO:0001411	N6_glycinylcarbamoyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641005	SO:0001305	SO:0001411	N6_threonylcarbamoyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641006	SO:0001306	SO:0001411	two_methylthio_N6_threonyl_carbamoyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641007	SO:0001307	SO:0001411	N6_methyl_N6_threonylcarbamoyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641008	SO:0001308	SO:0001411	N6_hydroxynorvalylcarbamoyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641009	SO:0001309	SO:0001411	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641010	SO:0001310	SO:0001411	two_prime_O_ribosyladenosine_phosphate	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641011	SO:0001311	SO:0001411	N6_N6_dimethyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641012	SO:0001312	SO:0001411	N6_2_prime_O_dimethyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641013	SO:0001313	SO:0001411	N6_N6_2_prime_O_trimethyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641014	SO:0001314	SO:0001411	one_two_prime_O_dimethyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	1641015	SO:0001315	SO:0001411	N6_acetyladenosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	SO	1641016	SO:0001316	SO:0001411	seven_deazaguanosine	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1641017	SO:0001317	SO:0001236	queuosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1641018	SO:0001318	SO:0001236	epoxyqueuosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1641019	SO:0001319	SO:0001236	galactosyl_queuosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1641020	SO:0001320	SO:0001236	mannosyl_queuosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1641021	SO:0001321	SO:0001236	seven_cyano_seven_deazaguanosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1641022	SO:0001322	SO:0001236	seven_aminomethyl_seven_deazaguanosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	1641023	SO:0001323	SO:0001236	archaeosine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641024	SO:0001324	SO:0001411	one_methylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641025	SO:0001325	SO:0001411	N2_methylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641026	SO:0001326	SO:0001411	seven_methylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641027	SO:0001327	SO:0001411	two_prime_O_methylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641028	SO:0001328	SO:0001411	N2_N2_dimethylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641029	SO:0001329	SO:0001411	N2_2_prime_O_dimethylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641030	SO:0001330	SO:0001411	N2_N2_2_prime_O_trimethylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641031	SO:0001331	SO:0001411	two_prime_O_ribosylguanosine_phosphate	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641032	SO:0001332	SO:0001411	wybutosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641033	SO:0001333	SO:0001411	peroxywybutosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641034	SO:0001334	SO:0001411	hydroxywybutosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641035	SO:0001335	SO:0001411	undermodified_hydroxywybutosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641036	SO:0001336	SO:0001411	wyosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641037	SO:0001337	SO:0001411	methylwyosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641038	SO:0001338	SO:0001411	N2_7_dimethylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641039	SO:0001339	SO:0001411	N2_N2_7_trimethylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641040	SO:0001340	SO:0001411	one_two_prime_O_dimethylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641041	SO:0001341	SO:0001411	four_demethylwyosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641042	SO:0001342	SO:0001411	isowyosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641043	SO:0001343	SO:0001411	N2_7_2prirme_O_trimethylguanosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641044	SO:0001344	SO:0001411	five_methyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641045	SO:0001345	SO:0001411	two_prime_O_methyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641046	SO:0001346	SO:0001411	five_two_prime_O_dimethyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641047	SO:0001347	SO:0001411	one_methylpseudouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641048	SO:0001348	SO:0001411	two_prime_O_methylpseudouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641049	SO:0001349	SO:0001411	two_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641050	SO:0001350	SO:0001411	four_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641051	SO:0001351	SO:0001411	five_methyl_2_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641052	SO:0001352	SO:0001411	two_thio_two_prime_O_methyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641053	SO:0001353	SO:0001411	three_three_amino_three_carboxypropyl_uridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641054	SO:0001354	SO:0001411	five_hydroxyuridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641055	SO:0001355	SO:0001411	five_methoxyuridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641056	SO:0001356	SO:0001411	uridine_five_oxyacetic_acid	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641057	SO:0001357	SO:0001411	uridine_five_oxyacetic_acid_methyl_ester	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641058	SO:0001358	SO:0001411	five_carboxyhydroxymethyl_uridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641059	SO:0001359	SO:0001411	five_carboxyhydroxymethyl_uridine_methyl_ester	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641060	SO:0001360	SO:0001411	five_methoxycarbonylmethyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641061	SO:0001361	SO:0001411	five_methoxycarbonylmethyl_two_prime_O_methyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641062	SO:0001362	SO:0001411	five_methoxycarbonylmethyl_two_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641063	SO:0001363	SO:0001411	five_aminomethyl_two_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641064	SO:0001364	SO:0001411	five_methylaminomethyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641065	SO:0001365	SO:0001411	five_methylaminomethyl_two_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641066	SO:0001366	SO:0001411	five_methylaminomethyl_two_selenouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641067	SO:0001367	SO:0001411	five_carbamoylmethyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641068	SO:0001368	SO:0001411	five_carbamoylmethyl_two_prime_O_methyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641069	SO:0001369	SO:0001411	five_carboxymethylaminomethyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641070	SO:0001370	SO:0001411	five_carboxymethylaminomethyl_two_prime_O_methyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641071	SO:0001371	SO:0001411	five_carboxymethylaminomethyl_two_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641072	SO:0001372	SO:0001411	three_methyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641073	SO:0001373	SO:0001411	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641074	SO:0001374	SO:0001411	five_carboxymethyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641075	SO:0001375	SO:0001411	three_two_prime_O_dimethyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641076	SO:0001376	SO:0001411	five_methyldihydrouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641077	SO:0001377	SO:0001411	three_methylpseudouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641078	SO:0001378	SO:0001411	five_taurinomethyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641079	SO:0001379	SO:0001411	five_taurinomethyl_two_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641080	SO:0001380	SO:0001411	five_isopentenylaminomethyl_uridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641081	SO:0001381	SO:0001411	five_isopentenylaminomethyl_two_thiouridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	1641082	SO:0001382	SO:0001411	five_isopentenylaminomethyl_two_prime_O_methyluridine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]	SO	1641083	SO:0001383	SO:0001411	histone_binding_site	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1641084	SO:0001384	SO:0000233	CDS_fragment	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	1641085	SO:0001384	SO:0000833	CDS_fragment	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1641086	SO:0001384	SO:0000833	CDS_fragment	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified glycine amino acid feature." [SO:ke]	SO	1805709	SO:0001386	SO:0000001	modified_glycine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified alanine amino acid feature." [SO:ke]	SO	1805710	SO:0001387	SO:0000001	modified_L_alanine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified asparagine amino acid feature." [SO:ke]	SO	1805711	SO:0001388	SO:0000001	modified_L_asparagine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified aspartic acid amino acid feature." [SO:ke]	SO	1805712	SO:0001389	SO:0000001	modified_L_aspartic_acid	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified cysteine amino acid feature." [SO:ke]	SO	1805713	SO:0001390	SO:0000001	modified_L_cysteine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1805714	SO:0001391	SO:0000001	modified_L_glutamic_acid	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified threonine amino acid feature." [SO:ke]	SO	1805715	SO:0001392	SO:0000001	modified_L_threonine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified tryptophan amino acid feature." [SO:ke]	SO	1805716	SO:0001393	SO:0000001	modified_L_tryptophan	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified glutamine amino acid feature." [SO:ke]	SO	1805717	SO:0001394	SO:0000001	modified_L_glutamine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified methionine amino acid feature." [SO:ke]	SO	1805718	SO:0001395	SO:0000001	modified_L_methionine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified isoleucine amino acid feature." [SO:ke]	SO	1805719	SO:0001396	SO:0000001	modified_L_isoleucine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified phenylalanine amino acid feature." [SO:ke]	SO	1805720	SO:0001397	SO:0000001	modified_L_phenylalanine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified histidine amino acid feature." [SO:ke]	SO	1805721	SO:0001398	SO:0000001	modified_L_histidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified serine amino acid feature." [SO:ke]	SO	1805722	SO:0001399	SO:0000001	modified_L_serine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified lysine amino acid feature." [SO:ke]	SO	1805723	SO:0001400	SO:0000001	modified_L_lysine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified leucine amino acid feature." [SO:ke]	SO	1805724	SO:0001401	SO:0000001	modified_L_leucine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified selenocysteine amino acid feature." [SO:ke]	SO	1805725	SO:0001402	SO:0000001	modified_L_selenocysteine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified valine amino acid feature." [SO:ke]	SO	1805726	SO:0001403	SO:0000001	modified_L_valine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified proline amino acid feature." [SO:ke]	SO	1805727	SO:0001404	SO:0000001	modified_L_proline	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified tyrosine amino acid feature." [SO:ke]	SO	1805728	SO:0001405	SO:0000001	modified_L_tyrosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post translationally modified arginine amino acid feature." [SO:ke]	SO	1805729	SO:0001406	SO:0000001	modified_L_arginine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]	SO	2165159	SO:0001408	SO:0000001	cleaved_for_gpi_anchor_region	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	1641130	SO:0001413	SO:0001411	translocation_breakpoint	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	1641131	SO:0001414	SO:0001411	insertion_breakpoint	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	1641132	SO:0001415	SO:0001411	deletion_breakpoint	SO:0000001
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	1641133	SO:0001419	SO:0000673	cis_splice_site	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	2441660	SO:0001419	SO:0001411	cis_splice_site	SO:0000001
5	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	1641135	SO:0001420	SO:0000673	trans_splice_site	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	2441661	SO:0001420	SO:0001411	trans_splice_site	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	1641137	SO:0001422	SO:0000839	conformational_switch	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	1641138	SO:0001422	SO:0000839	conformational_switch	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	2899073	SO:0001423	SO:0000001	dye_terminator_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	1641140	SO:0001423	SO:0000719	dye_terminator_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	2081957	SO:0001423	SO:0001876	dye_terminator_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read produced by the dye terminator method of sequencing." [SO:ke]	SO	2486357	SO:0001423	SO:0001248	dye_terminator_read	SO:0001410
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	2899074	SO:0001424	SO:0000001	pyrosequenced_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	1641144	SO:0001424	SO:0000719	pyrosequenced_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	2081960	SO:0001424	SO:0001876	pyrosequenced_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read produced by pyrosequencing technology." [SO:ke]	SO	2486358	SO:0001424	SO:0001248	pyrosequenced_read	SO:0001410
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	2899075	SO:0001425	SO:0000001	ligation_based_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	1641148	SO:0001425	SO:0000719	ligation_based_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	2081963	SO:0001425	SO:0001876	ligation_based_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read produced by ligation based sequencing technologies." [SO:ke]	SO	2486359	SO:0001425	SO:0001248	ligation_based_read	SO:0001410
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	2899076	SO:0001426	SO:0000001	polymerase_synthesis_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	1641152	SO:0001426	SO:0000719	polymerase_synthesis_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	2081966	SO:0001426	SO:0001876	polymerase_synthesis_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read produced by the polymerase based sequence by synthesis method." [SO:ke]	SO	2486360	SO:0001426	SO:0001248	polymerase_synthesis_read	SO:0001410
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]	SO	1641155	SO:0001427	SO:0001411	cis_regulatory_frameshift_element	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence assembly derived from expressed sequences." [SO:ke]	SO	1641156	SO:0001428	SO:0000001	expressed_sequence_assembly	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]	SO	1641157	SO:0001429	SO:0000001	DNA_binding_site	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]	SO	1641158	SO:0001433	SO:0001409	three_prime_RACE_clone	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]	SO	1641159	SO:0001434	SO:0000001	cassette_pseudogene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]	SO	1641160	SO:0001459	SO:0000001	CRISPR	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	2441664	SO:0001460	SO:0001411	insulator_binding_site	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	1641162	SO:0001460	SO:0005836	insulator_binding_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	2706848	SO:0001461	SO:0001411	enhancer_binding_site	SO:0000001
5	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	1641164	SO:0001461	SO:0001679	enhancer_binding_site	SO:0005836
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A collection of contigs." [SO:ke]	SO	1641165	SO:0001462	SO:0001410	contig_collection	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	1641166	SO:0001463	SO:0000673	lincRNA	SO:0000831
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	SO	1641167	SO:0001464	SO:0000695	UST	SO:0001409
5	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	1641168	SO:0001465	SO:0000696	three_prime_UST	SO:0000695
5	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	1641169	SO:0001466	SO:0000696	five_prime_UST	SO:0000695
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	1641170	SO:0001467	SO:0000695	RST	SO:0001409
5	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	1641171	SO:0001468	SO:0000696	three_prime_RST	SO:0000695
5	"A sequence used in experiment." [SO:ke]	\N	reagent	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	1641172	SO:0001469	SO:0000696	five_prime_RST	SO:0000695
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A match against an UST sequence." [SO:nlw]	SO	1641173	SO:0001470	SO:0001410	UST_match	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A match against an RST sequence." [SO:nlw]	SO	1641174	SO:0001471	SO:0001410	RST_match	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A nucleotide match to a primer sequence." [SO:nlw]	SO	1641175	SO:0001472	SO:0000001	primer_match	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	1641176	SO:0001473	SO:0000673	miRNA_antiguide	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	2441673	SO:0001473	SO:0001411	miRNA_antiguide	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	1641178	SO:0001475	SO:0000831	outron	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]	SO	2165168	SO:0001475	SO:0000001	outron	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]	SO	1641181	SO:0001477	SO:0001411	gene_trap_construct	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]	SO	1641183	SO:0001478	SO:0001411	promoter_trap_construct	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]	SO	1641185	SO:0001479	SO:0001411	enhancer_trap_construct	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	2899077	SO:0001480	SO:0000001	PAC_end	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	1641188	SO:0001480	SO:0000719	PAC_end	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	2081991	SO:0001480	SO:0001876	PAC_end	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	2486361	SO:0001480	SO:0001248	PAC_end	SO:0001410
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	1641191	SO:0001480	SO:0000695	PAC_end	SO:0001409
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	1641192	SO:0001480	SO:0001411	PAC_end	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]	SO	1641193	SO:0001481	SO:0000001	RAPD	SO:0000110
5	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	1641194	SO:0001482	SO:0001679	shadow_enhancer	SO:0005836
5	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	1641195	SO:0001484	SO:0000340	X_element_combinatorial_repeat	SO:0001235
5	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	1641197	SO:0001485	SO:0000340	Y_prime_element	SO:0001235
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	2165171	SO:0001492	SO:0001411	intronic_regulatory_region	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	1641200	SO:0001492	SO:0000673	intronic_regulatory_region	SO:0000831
5	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	1641201	SO:0001493	SO:0000830	centromere_DNA_Element_I	SO:0000340
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	1641202	SO:0001493	SO:0000830	centromere_DNA_Element_I	SO:0001411
5	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	1641203	SO:0001494	SO:0000830	centromere_DNA_Element_II	SO:0000340
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	1641204	SO:0001494	SO:0000830	centromere_DNA_Element_II	SO:0001411
5	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	1641205	SO:0001495	SO:0000830	centromere_DNA_Element_III	SO:0000340
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	1641206	SO:0001495	SO:0000830	centromere_DNA_Element_III	SO:0001411
5	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	1641207	SO:0001496	SO:0000340	telomeric_repeat	SO:0001235
5	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	1641209	SO:0001497	SO:0000340	X_element	SO:0001235
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	2441684	SO:0001497	SO:0001411	X_element	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	2899078	SO:0001498	SO:0000001	YAC_end	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	1641212	SO:0001498	SO:0000719	YAC_end	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	2082009	SO:0001498	SO:0001876	YAC_end	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	2486362	SO:0001498	SO:0001248	YAC_end	SO:0001410
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	1641215	SO:0001498	SO:0000695	YAC_end	SO:0001409
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	1641216	SO:0001498	SO:0001411	YAC_end	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]	SO	1641217	SO:0001503	SO:0000001	processed_transcript	SO:0000110
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome variation derived from an event during meiosis." [SO:ke]	SO	1641218	SO:0001504	SO:0001026	assortment_derived_variation	SO:0001260
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]	SO	1641219	SO:0001525	SO:0000001	assembly_error_correction	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]	SO	1641220	SO:0001526	SO:0000001	base_call_error_correction	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]	SO	1805738	SO:0001528	SO:0000001	nuclear_localization_signal	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the endosome." [SO:ke]	SO	1805739	SO:0001529	SO:0000001	endosomal_localization_signal	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]	SO	1805740	SO:0001530	SO:0000001	lysosomal_localization_signal	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]	SO	1805741	SO:0001531	SO:0000001	nuclear_export_signal	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region recognized by a recombinase." [SO:ke]	SO	1641229	SO:0001532	SO:0001411	recombination_signal_sequence	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	1641230	SO:0001533	SO:0000673	cryptic_splice_site	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	2441685	SO:0001533	SO:0001411	cryptic_splice_site	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]	SO	1805742	SO:0001534	SO:0000001	nuclear_rim_localization_signal	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	1641234	SO:0001535	SO:0001037	p_element	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	1641235	SO:0001535	SO:0001037	p_element	SO:0001411
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	1641236	SO:0001551	SO:0001536	increased_transcription_rate_variant	SO:0001060
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]	SO	1641237	SO:0001552	SO:0001536	decreased_transcription_rate_variant	SO:0001060
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]	SO	1641238	SO:0001560	SO:0001536	inactive_ligand_binding_site	SO:0001060
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]	SO	1641239	SO:0001561	SO:0001536	polypeptide_partial_loss_of_function	SO:0001060
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	1641240	SO:0001567	SO:0001576	stop_retained_variant	SO:0001564
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes the process of splicing." [SO:ke]	SO	1641241	SO:0001568	SO:0001537	splicing_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1641242	SO:0001569	SO:0001878	cryptic_splice_site_variant	SO:0001537
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	SO	1641243	SO:0001570	SO:0001564	cryptic_splice_acceptor	SO:0001878
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	SO	1641244	SO:0001571	SO:0001564	cryptic_splice_donor	SO:0001878
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby an exon is lost from the transcript." [SO:ke]	SO	1641245	SO:0001572	SO:0001878	exon_loss_variant	SO:0001537
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1641246	SO:0001573	SO:0001878	intron_gain	SO:0001537
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	1641247	SO:0001574	SO:0001564	splice_acceptor_variant	SO:0001878
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	1641248	SO:0001575	SO:0001564	splice_donor_variant	SO:0001878
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]	SO	1641249	SO:0001577	SO:0001537	complex_transcript_variant	SO:0001060
7	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	2165174	SO:0001578	SO:0001576	stop_lost	SO:0001564
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	1641253	SO:0001580	SO:0001878	coding_sequence_variant	SO:0001537
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	1641254	SO:0001582	SO:0001564	initiator_codon_variant	SO:0001878
5	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	1641255	SO:0001583	SO:0001580	missense_variant	SO:0001791
5	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	1641256	SO:0001583	SO:0001580	missense_variant	SO:0001968
5	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	1641257	SO:0001585	SO:0001818	conservative_missense_variant	SO:0001580
5	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	1641258	SO:0001586	SO:0001818	non_conservative_missense_variant	SO:0001580
5	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	1641259	SO:0001587	SO:0001580	stop_gained	SO:0001791
5	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	1641260	SO:0001587	SO:0001580	stop_gained	SO:0001968
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	1641261	SO:0001589	SO:0001576	frameshift_variant	SO:0001564
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	1641262	SO:0001590	SO:0001564	terminator_codon_variant	SO:0001878
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	1641263	SO:0001591	SO:0001791	frame_restoring_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	1641264	SO:0001591	SO:0001968	frame_restoring_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	1641265	SO:0001592	SO:0001791	minus_1_frameshift_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	1641266	SO:0001592	SO:0001968	minus_1_frameshift_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"" []	SO	1641267	SO:0001593	SO:0001791	minus_2_frameshift_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"" []	SO	1641268	SO:0001593	SO:0001968	minus_2_frameshift_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	1641269	SO:0001594	SO:0001791	plus_1_frameshift_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	1641270	SO:0001594	SO:0001968	plus_1_frameshift_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"" []	SO	1641271	SO:0001595	SO:0001791	plus_2_frameshift_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"" []	SO	1641272	SO:0001595	SO:0001968	plus_2_frameshift_variant	SO:0001576
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]	SO	1641273	SO:0001596	SO:0001537	transcript_secondary_structure_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]	SO	1641274	SO:0001597	SO:0001878	compensatory_transcript_secondary_structure_variant	SO:0001537
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]	SO	1641275	SO:0001603	SO:0001537	polypeptide_sequence_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]	SO	1641276	SO:0001604	SO:0001878	amino_acid_deletion	SO:0001537
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]	SO	1641277	SO:0001605	SO:0001878	amino_acid_insertion	SO:0001537
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	SO	1641278	SO:0001606	SO:0001878	amino_acid_substitution	SO:0001537
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	SO	1641279	SO:0001607	SO:0001564	conservative_amino_acid_substitution	SO:0001878
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	SO	1641280	SO:0001608	SO:0001564	non_conservative_amino_acid_substitution	SO:0001878
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	SO	1641281	SO:0001609	SO:0001878	elongated_polypeptide	SO:0001537
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	1641282	SO:0001610	SO:0001564	elongated_polypeptide_C_terminal	SO:0001878
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	1641283	SO:0001611	SO:0001564	elongated_polypeptide_N_terminal	SO:0001878
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	1641284	SO:0001612	SO:0001598	elongated_in_frame_polypeptide_C_terminal	SO:0001564
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	1641285	SO:0001613	SO:0001598	elongated_out_of_frame_polypeptide_C_terminal	SO:0001564
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	1641286	SO:0001614	SO:0001598	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001564
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	1641287	SO:0001615	SO:0001598	elongated_out_of_frame_polypeptide_N_terminal	SO:0001564
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]	SO	1641288	SO:0001616	SO:0001878	polypeptide_fusion	SO:0001537
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]	SO	1641289	SO:0001617	SO:0001878	polypeptide_truncation	SO:0001537
5	"A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]	\N	functional_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]	SO	1641290	SO:0001618	SO:0001539	inactive_catalytic_site	SO:0001536
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant of a non coding RNA gene." [SO:ke]	SO	1641291	SO:0001619	SO:0001537	non_coding_transcript_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant located with the sequence of the mature miRNA." [SO:ke]	SO	1641292	SO:0001620	SO:0001878	mature_miRNA_variant	SO:0001537
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A variant in a transcript that is the target of NMD." [SO:ke]	SO	1641293	SO:0001621	SO:0001537	NMD_transcript_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	1641294	SO:0001622	SO:0001878	UTR_variant	SO:0001537
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	1641295	SO:0001623	SO:0001564	5_prime_UTR_variant	SO:0001878
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	1641296	SO:0001624	SO:0001564	3_prime_UTR_variant	SO:0001878
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	1805743	SO:0001626	SO:0001576	incomplete_terminal_codon_variant	SO:0001564
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant occurring within an intron." [SO:ke]	SO	1641298	SO:0001627	SO:0001537	intron_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	1641299	SO:0001629	SO:0001878	splice_site_variant	SO:0001537
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]	SO	1641300	SO:0001630	SO:0001878	splice_region_variant	SO:0001537
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located within 5 KB of the end of a gene." [SO:ke]	SO	1641301	SO:0001633	SO:0001537	5KB_downstream_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located within a half KB of the end of a gene." [SO:ke]	SO	1641302	SO:0001634	SO:0001878	500B_downstream_variant	SO:0001537
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located within 5KB 5' of a gene." [SO:ke]	SO	1641303	SO:0001635	SO:0001537	5KB_upstream_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant located within 2KB 5' of a gene." [SO:ke]	SO	1641304	SO:0001636	SO:0001878	2KB_upstream_variant	SO:0001537
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes for ribosomal RNA." [SO:ke]	SO	1641305	SO:0001637	SO:0000001	rRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes for an piwi associated RNA." [SO:ke]	SO	1641306	SO:0001638	SO:0000001	piRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes an RNase P RNA." [SO:ke]	SO	1641307	SO:0001639	SO:0000001	RNase_P_RNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes a RNase_MRP_RNA." [SO:ke]	SO	1641308	SO:0001640	SO:0000001	RNase_MRP_RNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes large intervening non-coding RNA." [SO:ke]	SO	1641309	SO:0001641	SO:0000001	lincRNA_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]	SO	1641310	SO:0001643	SO:0000001	telomerase_RNA_gene	SO:0000110
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	2165175	SO:0001647	SO:0000233	kozak_sequence	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	2165176	SO:0001647	SO:0000833	kozak_sequence	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	2165177	SO:0001647	SO:0000833	kozak_sequence	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transposon that is disrupted by the insertion of another element." [SO:ke]	SO	2082071	SO:0001648	SO:0000001	nested_transposon	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposon that is disrupted by the insertion of another element." [SO:ke]	SO	1641319	SO:0001648	SO:0001411	nested_transposon	SO:0000001
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	1641320	SO:0001650	SO:0001576	inframe_variant	SO:0001564
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	2441721	SO:0001653	SO:0001411	retinoic_acid_responsive_element	SO:0000001
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	1641322	SO:0001653	SO:0005836	retinoic_acid_responsive_element	SO:0000831
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	1641323	SO:0001654	SO:0000001	nucleotide_to_protein_binding_site	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]	SO	1641324	SO:0001658	SO:0000001	nested_tandem_repeat	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1641325	SO:0001659	SO:0001411	promoter_element	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1641326	SO:0001660	SO:0001683	core_promoter_element	SO:0001411
5	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	1641327	SO:0001661	SO:0000713	RNA_polymerase_II_TATA_box	SO:0000714
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	1641328	SO:0001661	SO:0000167	RNA_polymerase_II_TATA_box	SO:0001055
5	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	1641329	SO:0001662	SO:0000713	RNA_polymerase_III_TATA_box	SO:0000714
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	1641330	SO:0001662	SO:0001055	RNA_polymerase_III_TATA_box	SO:0001679
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	1641331	SO:0001663	SO:0000714	BREd_motif	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	1641332	SO:0001663	SO:0000167	BREd_motif	SO:0001055
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	1641333	SO:0001664	SO:0000714	DCE	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	1641334	SO:0001664	SO:0000167	DCE	SO:0001055
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	3056748	SO:0001665	SO:0001411	DCE_SI	SO:0000001
5	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	1641337	SO:0001665	SO:0001203	DCE_SI	SO:0000167
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	3056749	SO:0001666	SO:0001411	DCE_SII	SO:0000001
5	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	1641340	SO:0001666	SO:0001203	DCE_SII	SO:0000167
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	3056750	SO:0001667	SO:0001411	DCE_SIII	SO:0000001
5	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	\N	promoter	SOFA	\N	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	1641343	SO:0001667	SO:0001203	DCE_SIII	SO:0000167
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	1641344	SO:0001668	SO:0000714	proximal_promoter_element	SO:0001683
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	1641345	SO:0001669	SO:0001055	RNApol_II_core_promoter	SO:0001679
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"" []	SO	1641346	SO:0001670	SO:0000714	distal_promoter_element	SO:0001683
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2165178	SO:0001671	SO:0005836	bacterial_RNApol_promoter_sigma_70	SO:0000831
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1641348	SO:0001671	SO:0001055	bacterial_RNApol_promoter_sigma_70	SO:0001679
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2165179	SO:0001672	SO:0005836	bacterial_RNApol_promoter_sigma54	SO:0000831
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"" []	SO	1641350	SO:0001672	SO:0001055	bacterial_RNApol_promoter_sigma54	SO:0001679
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2961220	SO:0001673	SO:0001411	minus_12_signal	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2441740	SO:0001673	SO:0001679	minus_12_signal	SO:0005836
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	1641353	SO:0001673	SO:0000167	minus_12_signal	SO:0001055
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2961221	SO:0001674	SO:0001411	minus_24_signal	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2441742	SO:0001674	SO:0001679	minus_24_signal	SO:0005836
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	1641356	SO:0001674	SO:0000167	minus_24_signal	SO:0001055
5	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	1641357	SO:0001675	SO:0000713	A_box_type_1	SO:0000714
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	1641358	SO:0001675	SO:0000167	A_box_type_1	SO:0001055
5	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	1641359	SO:0001676	SO:0000713	A_box_type_2	SO:0000714
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	1641360	SO:0001676	SO:0000167	A_box_type_2	SO:0001055
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	1641361	SO:0001677	SO:0000714	intermediate_element	SO:0001683
5	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	1641362	SO:0001677	SO:0000167	intermediate_element	SO:0001055
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	SO	1641363	SO:0001678	SO:0001683	regulatory_promoter_element	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	SO	1641364	SO:0001679	SO:0000001	transcription_regulatory_region	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of translation." [SO:ke]	SO	1641365	SO:0001680	SO:0000001	translation_regulatory_region	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of recombination." [SO:ke]	SO	1641366	SO:0001681	SO:0000001	recombination_regulatory_region	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]	SO	1641367	SO:0001682	SO:0000001	replication_regulatory_region	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	1641368	SO:0001689	SO:0001411	five_prime_restriction_enzyme_junction	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1641369	SO:0001690	SO:0001411	three_prime_restriction_enzyme_junction	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1641370	SO:0001691	SO:0000001	blunt_end_restriction_enzyme_cleavage_site	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	1641371	SO:0001692	SO:0000001	sticky_end_restriction_enzyme_cleavage_site	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	1641372	SO:0001693	SO:0001411	blunt_end_restriction_enzyme_cleavage_junction	SO:0000001
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	SO	1641373	SO:0001698	SO:0000695	ASPE_primer	SO:0001409
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	SO	1641374	SO:0001699	SO:0000695	dCAPS_primer	SO:0001409
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	1641375	SO:0001700	SO:0100021	histone_modification	SO:0000839
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	1641376	SO:0001701	SO:0001067	histone_methylation_site	SO:0100021
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	2899079	SO:0001701	SO:0000001	histone_methylation_site	SO:0000110
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	1641378	SO:0001702	SO:0001067	histone_acetylation_site	SO:0100021
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	2899080	SO:0001702	SO:0000001	histone_acetylation_site	SO:0000110
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641380	SO:0001703	SO:0001089	H3K9_acetylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641381	SO:0001703	SO:0001720	H3K9_acetylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641382	SO:0001704	SO:0001089	H3K14_acetylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641383	SO:0001704	SO:0001720	H3K14_acetylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641384	SO:0001705	SO:0001089	H3K4_monomethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641385	SO:0001705	SO:0001720	H3K4_monomethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641386	SO:0001706	SO:0001089	H3K4_trimethylation	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641387	SO:0001706	SO:0001720	H3K4_trimethylation	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641388	SO:0001707	SO:0001089	H3K9_trimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641389	SO:0001707	SO:0001720	H3K9_trimethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641390	SO:0001708	SO:0001089	H3K27_monomethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641391	SO:0001708	SO:0001720	H3K27_monomethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641392	SO:0001709	SO:0001089	H3K27_trimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641393	SO:0001709	SO:0001720	H3K27_trimethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641394	SO:0001710	SO:0001089	H3K79_monomethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641395	SO:0001710	SO:0001720	H3K79_monomethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641396	SO:0001711	SO:0001089	H3K79_dimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641397	SO:0001711	SO:0001720	H3K79_dimethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641398	SO:0001712	SO:0001089	H3K79_trimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641399	SO:0001712	SO:0001720	H3K79_trimethylation_site	SO:0001411
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641400	SO:0001713	SO:0100001	H4K20_monomethylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995417	SO:0001713	SO:0001411	H4K20_monomethylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	1641402	SO:0001714	SO:0100001	H2BK5_monomethylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995418	SO:0001714	SO:0001411	H2BK5_monomethylation_site	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	SO	1641404	SO:0001715	SO:0000831	ISRE	SO:0001411
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	1641405	SO:0001716	SO:0001067	histone_ubiqitination_site	SO:0100021
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	2899081	SO:0001716	SO:0000001	histone_ubiqitination_site	SO:0000110
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	1641407	SO:0001717	SO:0100001	H2B_ubiquitination_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	2995419	SO:0001717	SO:0001411	H2B_ubiquitination_site	SO:0000001
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1641409	SO:0001718	SO:0001089	H3K18_acetylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1641410	SO:0001718	SO:0001720	H3K18_acetylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1641411	SO:0001719	SO:0001089	H3K23_acylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1641412	SO:0001719	SO:0001720	H3K23_acylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1641413	SO:0001721	SO:0001089	H3K27_acylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	1641414	SO:0001721	SO:0001720	H3K27_acylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	1641415	SO:0001722	SO:0001089	H3K36_monomethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	1641416	SO:0001722	SO:0001720	H3K36_monomethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	1641417	SO:0001723	SO:0001089	H3K36_dimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	1641418	SO:0001723	SO:0001720	H3K36_dimethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	1641419	SO:0001724	SO:0001089	H3K36_trimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	1641420	SO:0001724	SO:0001720	H3K36_trimethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	1641421	SO:0001725	SO:0001089	H3K4_dimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	1641422	SO:0001725	SO:0001720	H3K4_dimethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	1641423	SO:0001726	SO:0001089	H3K27_dimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	1641424	SO:0001726	SO:0001720	H3K27_dimethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	1641425	SO:0001727	SO:0001089	H3K9_monomethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	1641426	SO:0001727	SO:0001720	H3K9_monomethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	1641427	SO:0001728	SO:0001089	H3K9_dimethylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	1641428	SO:0001728	SO:0001720	H3K9_dimethylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	1641429	SO:0001729	SO:0001089	H4K16_acylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	1641430	SO:0001729	SO:0001720	H4K16_acylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	1641431	SO:0001730	SO:0001089	H4K5_acylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	1641432	SO:0001730	SO:0001720	H4K5_acylation_site	SO:0001411
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	1641433	SO:0001731	SO:0001089	H4K8_acylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	1641434	SO:0001731	SO:0001720	H4K8_acylation_site	SO:0001411
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1641435	SO:0001732	SO:0100001	H3K27_methylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2995446	SO:0001732	SO:0001411	H3K27_methylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1641437	SO:0001733	SO:0100001	H3K36_methylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2995447	SO:0001733	SO:0001411	H3K36_methylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	1641439	SO:0001734	SO:0100001	H3K4_methylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	2995448	SO:0001734	SO:0001411	H3K4_methylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1641441	SO:0001735	SO:0100001	H3K79_methylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2995449	SO:0001735	SO:0001411	H3K79_methylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	1641443	SO:0001736	SO:0100001	H3K9_methylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2995450	SO:0001736	SO:0001411	H3K9_methylation_site	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	1641445	SO:0001737	SO:0001067	histone_acylation_region	SO:0100021
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	2899082	SO:0001737	SO:0000001	histone_acylation_region	SO:0000110
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	1641447	SO:0001738	SO:0100001	H4K_acylation_region	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	2995451	SO:0001738	SO:0001411	H4K_acylation_region	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene with a translational start codon of CUG." [SO:mc]	SO	1641449	SO:0001740	SO:0000001	gene_with_start_codon_CUG	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]	SO	1805744	SO:0001741	SO:0000001	pseudogenic_gene_segment	SO:0000110
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641452	SO:0001748	SO:0000162	SL3_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641453	SO:0001749	SO:0000162	SL4_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641454	SO:0001750	SO:0000162	SL5_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641455	SO:0001751	SO:0000162	SL6_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641456	SO:0001752	SO:0000162	SL7_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641457	SO:0001753	SO:0000162	SL8_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641458	SO:0001754	SO:0000162	SL9_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641459	SO:0001755	SO:0000162	SL10_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641460	SO:0001756	SO:0000162	SL11_acceptor_site	SO:0000835
5	"A part of a primary transcript." [SO:ke]	\N	primary_transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	1641461	SO:0001757	SO:0000162	SL12_acceptor_site	SO:0000835
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]	SO	1641462	SO:0001758	SO:0000001	duplicated_pseudogene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]	SO	1641463	SO:0001759	SO:0000001	unitary_pseudogene	SO:0000110
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	1641464	SO:0001787	SO:0001564	splice_donor_5th_base_variant	SO:0001878
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	1641465	SO:0001788	SO:0001039	U_box	SO:0001037
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes exon sequence." [SO:ke]	SO	1641466	SO:0001791	SO:0001537	exon_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	1641467	SO:0001792	SO:0001878	non_coding_transcript_exon_variant	SO:0001537
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	2899083	SO:0001793	SO:0000001	clone_end	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	1641469	SO:0001793	SO:0000719	clone_end	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	2082211	SO:0001793	SO:0001876	clone_end	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A read from an end of the clone sequence." [SO:ke]	SO	2486366	SO:0001793	SO:0001248	clone_end	SO:0001410
5	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	1641472	SO:0001794	SO:0000340	point_centromere	SO:0001235
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	2441851	SO:0001794	SO:0001411	point_centromere	SO:0000001
5	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	1641474	SO:0001795	SO:0000340	regional_centromere	SO:0001235
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	2441852	SO:0001795	SO:0001411	regional_centromere	SO:0000001
5	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	1641476	SO:0001796	SO:0000830	regional_centromere_central_core	SO:0000340
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	1641477	SO:0001796	SO:0000830	regional_centromere_central_core	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	2899084	SO:0001798	SO:0000001	regional_centromere_inner_repeat_region	SO:0000110
5	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	1641479	SO:0001798	SO:0000628	regional_centromere_inner_repeat_region	SO:0000830
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	2731424	SO:0001799	SO:0000001	regional_centromere_outer_repeat_region	SO:0000110
5	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	1641481	SO:0001799	SO:0000830	regional_centromere_outer_repeat_region	SO:0000340
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	1641482	SO:0001799	SO:0000830	regional_centromere_outer_repeat_region	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	SO	1641483	SO:0001800	SO:0000831	tasiRNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a tasiRNA." [PMID:16145017]	SO	1641484	SO:0001801	SO:0000831	tasiRNA_primary_transcript	SO:0001411
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]	SO	1641485	SO:0001802	SO:0001536	increased_polyadenylation_variant	SO:0001060
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]	SO	1641486	SO:0001803	SO:0001536	decreased_polyadenylation_variant	SO:0001060
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	2885890	SO:0001804	SO:0001411	DDB_box	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	1641488	SO:0001804	SO:0001067	DDB_box	SO:0100021
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	1641489	SO:0001805	SO:0000839	destruction_box	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	1641490	SO:0001805	SO:0000839	destruction_box	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]	SO	1805746	SO:0001806	SO:0000001	ER_retention_signal	SO:0000110
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	1641493	SO:0001807	SO:0000839	KEN_box	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	1641494	SO:0001807	SO:0000839	KEN_box	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]	SO	1805747	SO:0001808	SO:0000001	mitochondrial_targeting_signal	SO:0000110
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens,SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	1641499	SO:0001809	SO:0001063	signal_anchor	SO:0000839
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	2165183	SO:0001809	SO:0000104	signal_anchor	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	2548858	SO:0001809	SO:0001411	signal_anchor	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	2885891	SO:0001810	SO:0001411	PIP_box	SO:0000001
5	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	1641503	SO:0001810	SO:0001067	PIP_box	SO:0100021
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	1641504	SO:0001811	SO:0100021	phosphorylation_site	SO:0000839
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	1805750	SO:0001812	SO:0000839	transmembrane_helix	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	1805751	SO:0001812	SO:0000839	transmembrane_helix	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]	SO	1805752	SO:0001813	SO:0000001	vacuolar_sorting_signal	SO:0000110
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	1641510	SO:0001818	SO:0001564	protein_altering_variant	SO:0001878
5	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	1641511	SO:0001819	SO:0001564	synonymous_variant	SO:0001878
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	1641512	SO:0001820	SO:0001791	inframe_indel	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	1641513	SO:0001820	SO:0001968	inframe_indel	SO:0001576
5	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	1641514	SO:0001821	SO:0001580	inframe_insertion	SO:0001791
5	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	1641515	SO:0001821	SO:0001580	inframe_insertion	SO:0001968
10	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	2899085	SO:0001821	SO:0001537	inframe_insertion	SO:0001060
5	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	1641517	SO:0001822	SO:0001580	inframe_deletion	SO:0001791
5	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	1641518	SO:0001822	SO:0001580	inframe_deletion	SO:0001968
5	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	1641519	SO:0001823	SO:0001818	conservative_inframe_insertion	SO:0001580
10	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	2995462	SO:0001823	SO:0001878	conservative_inframe_insertion	SO:0001537
5	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	1641521	SO:0001824	SO:0001818	disruptive_inframe_insertion	SO:0001580
10	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	2995463	SO:0001824	SO:0001878	disruptive_inframe_insertion	SO:0001537
5	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	1641523	SO:0001825	SO:0001818	conservative_inframe_deletion	SO:0001580
11	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	3002355	SO:0001825	SO:0001537	conservative_inframe_deletion	SO:0001060
5	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	1641525	SO:0001826	SO:0001818	disruptive_inframe_deletion	SO:0001580
11	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	3002356	SO:0001826	SO:0001537	disruptive_inframe_deletion	SO:0001060
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	2899086	SO:0001827	SO:0000001	mRNA_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	1641528	SO:0001827	SO:0000719	mRNA_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	2082258	SO:0001827	SO:0001876	mRNA_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequencer read of an mRNA substrate." [SO:ke]	SO	2486368	SO:0001827	SO:0001248	mRNA_read	SO:0001410
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	2899087	SO:0001828	SO:0000001	genomic_DNA_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	1641532	SO:0001828	SO:0000719	genomic_DNA_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	2082261	SO:0001828	SO:0001876	genomic_DNA_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequencer read of a genomic DNA substrate." [SO:ke]	SO	2486369	SO:0001828	SO:0001248	genomic_DNA_read	SO:0001410
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A contig composed of mRNA_reads." [SO:ke]	SO	2731427	SO:0001829	SO:0000001	mRNA_contig	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]	SO	1641539	SO:0001830	SO:0000001	AFLP_fragment	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A match to a protein HMM such as pfam." [SO:ke]	SO	1641540	SO:0001831	SO:0000001	protein_hmm_match	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The variable region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	1805757	SO:0001833	SO:0000001	V_region	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The constant region of an immunoglobulin polypeptide sequence." [SO:ke]	SO	1805758	SO:0001834	SO:0000001	C_region	SO:0000110
5	"" []	\N	recombination_feature	\N	\N	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	1641545	SO:0001835	SO:0000669	N_region	SO:0000298
5	"" []	\N	recombination_feature	\N	\N	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	1641546	SO:0001836	SO:0000669	S_region	SO:0000298
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	SO	1641547	SO:0001839	SO:0001683	CSL_response_element	SO:0001411
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	1641548	SO:0001840	SO:0000714	GATA_box	SO:0001683
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	SO	1641549	SO:0001842	SO:0001683	AP_1_binding_site	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	SO	1641550	SO:0001843	SO:0001683	CRE	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	SO	1641551	SO:0001844	SO:0001683	CuRE	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	SO	1641552	SO:0001845	SO:0001683	DRE	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	SO	1641553	SO:0001846	SO:0001683	FLEX_element	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	SO	1641554	SO:0001847	SO:0001683	forkhead_motif	SO:0001411
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	1641555	SO:0001848	SO:0000714	homol_D_box	SO:0001683
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	SO	1641556	SO:0001849	SO:0001683	homol_E_box	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	SO	1641557	SO:0001850	SO:0001683	HSE	SO:0001411
5	"A region of nucleotide sequence corresponding to a known motif." [SO:ke]	\N	nucleotide_motif	SOFA	\N	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	1641558	SO:0001851	SO:0000713	iron_repressed_GATA_element	SO:0000714
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	SO	1641559	SO:0001852	SO:0001683	mating_type_M_box	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]	SO	1641560	SO:0001853	SO:0001411	androgen_response_element	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]	SO	1641561	SO:0001854	SO:0001409	smFISH_probe	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	SO	1641562	SO:0001855	SO:0001683	MCB	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	SO	1641563	SO:0001856	SO:0001683	CCAAT_motif	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	SO	1641564	SO:0001857	SO:0001683	Ace2_UAS	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	SO	1641565	SO:0001858	SO:0001683	TR_box	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	SO	1641566	SO:0001859	SO:0001683	STREP_motif	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]	SO	1641567	SO:0001860	SO:0001411	rDNA_intergenic_spacer_element	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	SO	1641568	SO:0001861	SO:0001683	sterol_regulatory_element	SO:0001411
5	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	1641569	SO:0001862	SO:0000705	GT_dinucleotide_repeat	SO:0000657
5	"A region of sequence containing one or more repeat units." [SO:ke]	\N	repeat_region	SOFA	SOFA	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	1641570	SO:0001863	SO:0000705	GTT_trinucleotide_repeat	SO:0000657
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]	SO	1641571	SO:0001864	SO:0001411	Sap1_recognition_motif	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	SO	1641572	SO:0001865	SO:0001683	CDRE_motif	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	2731428	SO:0001866	SO:0000001	BAC_read_contig	SO:0000110
5	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	1641577	SO:0001866	SO:0000695	BAC_read_contig	SO:0001409
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	1641578	SO:0001866	SO:0001411	BAC_read_contig	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]	SO	1641579	SO:0001868	SO:0000001	positional_candidate_gene	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]	SO	1641580	SO:0001869	SO:0000001	functional_candidate_gene	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	SO	1641581	SO:0001870	SO:0000831	enhancerRNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	SO	1641582	SO:0001871	SO:0001683	PCB	SO:0001411
6	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	1805761	SO:0001875	SO:0001248	unassigned_supercontig	SO:0001410
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	SO	1641584	SO:0001876	SO:0000001	partial_genomic_sequence_assembly	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	SO	1641585	SO:0001877	SO:0000831	lnc_RNA	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	1641586	SO:0001896	SO:0000233	transposable_element_CDS	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	1641587	SO:0001896	SO:0000833	transposable_element_CDS	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	1641588	SO:0001896	SO:0000833	transposable_element_CDS	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	2764397	SO:0001896	SO:0000001	transposable_element_CDS	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	2706993	SO:0001896	SO:0001411	transposable_element_CDS	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2899088	SO:0001898	SO:0000001	dg_repeat	SO:0000110
5	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	1641594	SO:0001898	SO:0000628	dg_repeat	SO:0000830
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2899089	SO:0001899	SO:0000001	dh_repeat	SO:0000110
5	"A region of a chromosome." [SO:ke]	\N	chromosome_part	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	1641596	SO:0001899	SO:0000628	dh_repeat	SO:0000830
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]	SO	1641597	SO:0001900	SO:0001411	M26_binding_site	SO:0000001
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	1641598	SO:0001901	SO:0000714	AACCCT_box	SO:0001683
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]	SO	2165191	SO:0001902	SO:0000001	splice_region	SO:0000110
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	1641601	SO:0001903	SO:0000673	intronic_lncRNA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	1641602	SO:0001904	SO:0000673	antisense_lncRNA	SO:0000831
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]	SO	1641603	SO:0001905	SO:0001411	regional_centromere_outer_repeat_transcript	SO:0000001
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	1641604	SO:0001909	SO:0001791	frameshift_elongation	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	1641605	SO:0001909	SO:0001968	frameshift_elongation	SO:0001576
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	2731429	SO:0001909	SO:0001537	frameshift_elongation	SO:0001060
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	1641607	SO:0001910	SO:0001791	frameshift_truncation	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	1641608	SO:0001910	SO:0001968	frameshift_truncation	SO:0001576
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	2165192	SO:0001913	SO:0005836	bacterial_RNApol_promoter_sigma_ecf	SO:0000831
5	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	1641610	SO:0001913	SO:0001055	bacterial_RNApol_promoter_sigma_ecf	SO:0001679
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]	SO	1641611	SO:0001914	SO:0001411	rDNA_replication_fork_barrier	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]	SO	1641612	SO:0001916	SO:0001409	CAGE_tag	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	1641613	SO:0001918	SO:0001236	5_methylcytosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	1641614	SO:0001918	SO:0001720	5_methylcytosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	1641615	SO:0001919	SO:0001236	4_methylcytosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	1641616	SO:0001919	SO:0001720	4_methylcytosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	1641617	SO:0001920	SO:0001236	N6_methyladenine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	1641618	SO:0001920	SO:0001720	N6_methyladenine	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A contig of mitochondria derived sequences." [GMOD:ea]	SO	2731430	SO:0001921	SO:0000001	mitochondrial_contig	SO:0000110
6	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	1805768	SO:0001922	SO:0001248	mitochondrial_supercontig	SO:0001410
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	1641624	SO:0001923	SO:0000673	TERRA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	1641625	SO:0001924	SO:0000673	ARRET	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	1641626	SO:0001925	SO:0000673	ARIA	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	1641627	SO:0001926	SO:0000673	anti_ARRET	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	SO	1641628	SO:0001927	SO:0000831	telomeric_transcript	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A duplication of the distal region of a chromosome." [SO:bm]	SO	1641629	SO:0001928	SO:0000001	distal_duplication	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	2899090	SO:0001929	SO:0000001	mitochondrial_DNA_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	1641631	SO:0001929	SO:0000719	mitochondrial_DNA_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	2082324	SO:0001929	SO:0001876	mitochondrial_DNA_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequencer read of a mitochondrial DNA sample." [GMOD:ea]	SO	2486378	SO:0001929	SO:0001248	mitochondrial_DNA_read	SO:0001410
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	2899091	SO:0001930	SO:0000001	chloroplast_DNA_read	SO:0000110
5	"A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]	\N	partial_genomic_sequence_assembly	\N	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	1641635	SO:0001930	SO:0000719	chloroplast_DNA_read	SO:0001876
6	"A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]	\N	sequence_assembly	SOFA	\N	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	2082327	SO:0001930	SO:0001876	chloroplast_DNA_read	SO:0000353
8	"A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]	\N	experimental_feature	SOFA	SOFA	sequence	"A sequencer read of a chloroplast DNA sample." [GMOD:ea]	SO	2486379	SO:0001930	SO:0001248	chloroplast_DNA_read	SO:0001410
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]	SO	2165198	SO:0001932	SO:0000001	restriction_enzyme_five_prime_single_strand_overhang	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]	SO	2165199	SO:0001933	SO:0000001	restriction_enzyme_three_prime_single_strand_overhang	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]	SO	1641642	SO:0001934	SO:0000001	monomeric_repeat	SO:0000110
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	1641643	SO:0001935	SO:0100001	H3K20_trimethylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	2995466	SO:0001935	SO:0001411	H3K20_trimethylation_site	SO:0000001
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	1641645	SO:0001936	SO:0001089	H3K36_acetylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	1641646	SO:0001936	SO:0001720	H3K36_acetylation_site	SO:0001411
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	1641647	SO:0001937	SO:0100001	H2BK12_acetylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	2995469	SO:0001937	SO:0001411	H2BK12_acetylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	1641649	SO:0001938	SO:0100001	H2AK5_acetylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2995470	SO:0001938	SO:0001411	H2AK5_acetylation_site	SO:0000001
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	1641651	SO:0001939	SO:0001089	H4K12_acetylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	1641652	SO:0001939	SO:0001720	H4K12_acetylation_site	SO:0001411
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1641653	SO:0001940	SO:0100001	H2BK120_acetylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2995473	SO:0001940	SO:0001411	H2BK120_acetylation_site	SO:0000001
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	1641655	SO:0001941	SO:0001089	H4K91_acetylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	1641656	SO:0001941	SO:0001720	H4K91_acetylation_site	SO:0001411
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1641657	SO:0001942	SO:0100001	H2BK20_acetylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2995476	SO:0001942	SO:0001411	H2BK20_acetylation_site	SO:0000001
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	1641659	SO:0001943	SO:0001089	H3K4ac_acetylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	1641660	SO:0001943	SO:0001720	H3K4ac_acetylation_site	SO:0001411
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	1641661	SO:0001944	SO:0100001	H2AK9_acetylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2995479	SO:0001944	SO:0001411	H2AK9_acetylation_site	SO:0000001
5	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	\N	biochemical_region_of_peptide	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	1641663	SO:0001945	SO:0001089	H3K56_acetylation_site	SO:0100001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	1641664	SO:0001945	SO:0001720	H3K56_acetylation_site	SO:0001411
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	1641665	SO:0001946	SO:0100001	H2BK15_acetylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2995482	SO:0001946	SO:0001411	H2BK15_acetylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	1641667	SO:0001947	SO:0100001	H3R2_monomethylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	2995483	SO:0001947	SO:0001411	H3R2_monomethylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	1641669	SO:0001948	SO:0100001	H3R2_dimethylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2995484	SO:0001948	SO:0001411	H3R2_dimethylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	1641671	SO:0001949	SO:0100001	H4R3_dimethylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	2995485	SO:0001949	SO:0001411	H4R3_dimethylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	1641673	SO:0001950	SO:0100001	H4K4_trimethylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	2995486	SO:0001950	SO:0001411	H4K4_trimethylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	1641675	SO:0001951	SO:0100001	H3K23_dimethylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2995487	SO:0001951	SO:0001411	H3K23_dimethylation_site	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	SO	1641677	SO:0001952	SO:0000831	promoter_flanking_region	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	1641678	SO:0001958	SO:0000673	lariat_intron	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	2441956	SO:0001958	SO:0001411	lariat_intron	SO:0000001
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	1641680	SO:0001959	SO:0000714	TCT_motif	SO:0001683
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	1641681	SO:0001960	SO:0001236	5_hydroxymethylcytosine	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	1641682	SO:0001960	SO:0001720	5_hydroxymethylcytosine	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	1641683	SO:0001961	SO:0001411	5_formylcytosine	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified adenine DNA base feature." [SO:ke]	SO	1641684	SO:0001962	SO:0000001	modified_adenine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified cytosine DNA base feature." [SO:ke]	SO	1641685	SO:0001963	SO:0000001	modified_cytosine	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified guanine DNA base feature." [SO:ke]	SO	1641686	SO:0001964	SO:0000001	modified_guanine	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	1641687	SO:0001965	SO:0001411	8_oxoguanine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	1641688	SO:0001966	SO:0001411	5_carboxylcytosine	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	1641689	SO:0001967	SO:0001411	8_oxoadenine	SO:0000001
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant of a protein coding gene." [SO:ke]	SO	1641690	SO:0001968	SO:0001537	coding_transcript_variant	SO:0001060
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	1641691	SO:0001969	SO:0001878	coding_transcript_intron_variant	SO:0001537
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	1641692	SO:0001970	SO:0001878	non_coding_transcript_intron_variant	SO:0001537
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	1641693	SO:0001971	SO:0001411	zinc_finger_binding_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	1641694	SO:0001972	SO:0100001	histone_4_acylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2995488	SO:0001972	SO:0001411	histone_4_acylation_site	SO:0000001
5	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	1641696	SO:0001973	SO:0100001	histone_3_acetylation_site	SO:0001067
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2995489	SO:0001973	SO:0001411	histone_3_acetylation_site	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	SO	1641698	SO:0001974	SO:0001683	CTCF_binding_site	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]	SO	1641699	SO:0001975	SO:0001411	five_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]	SO	1641700	SO:0001976	SO:0001411	three_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A motif that affects the stability of RNA." [PMID:22495308, SO:ke]	SO	1641702	SO:0001979	SO:0001411	RNA_stability_element	SO:0000001
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	1641703	SO:0001980	SO:0000714	G_box	SO:0001683
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	1641704	SO:0001981	SO:0000714	L_box	SO:0001683
5	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	1641705	SO:0001982	SO:0000714	I-box	SO:0001683
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	1641706	SO:0001983	SO:0001576	5_prime_UTR_premature_start_codon_variant	SO:0001564
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]	SO	1641707	SO:0001984	SO:0000001	silent_mating_type_cassette_array	SO:0000110
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	1641708	SO:0001988	SO:0001791	5_prime_UTR_premature_start_codon_gain_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	1641709	SO:0001988	SO:0001968	5_prime_UTR_premature_start_codon_gain_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	1641710	SO:0001989	SO:0001791	5_prime_UTR_premature_start_codon_loss_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	1641711	SO:0001989	SO:0001968	5_prime_UTR_premature_start_codon_loss_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	1641712	SO:0001990	SO:0001791	five_prime_UTR_premature_start_codon_location_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	1641713	SO:0001990	SO:0001968	five_prime_UTR_premature_start_codon_location_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	1641714	SO:0001992	SO:0001791	nonsynonymous_variant	SO:0001576
5	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	1641715	SO:0001992	SO:0001968	nonsynonymous_variant	SO:0001576
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	1641716	SO:0001993	SO:0000185	extended_cis_splice_site	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	1641717	SO:0001993	SO:0000833	extended_cis_splice_site	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	1641718	SO:0001993	SO:0000833	extended_cis_splice_site	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	2165200	SO:0001994	SO:0000673	intron_base_5	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	2806661	SO:0001994	SO:0001411	intron_base_5	SO:0000001
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]	SO	1641723	SO:0001995	SO:0001878	extended_intronic_splice_region_variant	SO:0001537
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	1805773	SO:0001996	SO:0000673	extended_intronic_splice_region	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	2625402	SO:0001996	SO:0001411	extended_intronic_splice_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	1641726	SO:0001997	SO:0001235	subtelomere	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]	SO	2165202	SO:0001997	SO:0000001	subtelomere	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]	SO	1641728	SO:0001998	SO:0000001	sgRNA	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"DNA motif that is a component of a mating type region." [SO:ke]	SO	1805775	SO:0001999	SO:0000001	mating_type_region_motif	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	1641731	SO:0002000	SO:0001683	W_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	2082400	SO:0002000	SO:0001411	W_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	1641733	SO:0002001	SO:0001683	Y_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	2082402	SO:0002001	SO:0001411	Y_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1641735	SO:0002002	SO:0001683	Z1_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	2082404	SO:0002002	SO:0001411	Z1_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	1641737	SO:0002003	SO:0001683	Z2_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	2082406	SO:0002003	SO:0001411	Z2_region	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]	SO	1805776	SO:0002004	SO:0000001	ARS_consensus_sequence	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]	SO	1641741	SO:0002005	SO:0001411	DSR_motif	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	SO	1641742	SO:0002006	SO:0001683	zinc_repressed_element	SO:0001411
5	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	1641743	SO:0002008	SO:0001650	rare_amino_acid_variant	SO:0001818
5	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	1641744	SO:0002009	SO:0001992	selenocysteine_loss	SO:0001650
5	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	\N	inframe_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	1641745	SO:0002010	SO:0001992	pyrrolysine_loss	SO:0001650
5	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence." [SO:ke]	SO	1641746	SO:0002011	SO:0001537	intragenic_variant	SO:0001060
7	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	2165203	SO:0002012	SO:0001576	start_lost	SO:0001564
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	1641750	SO:0002013	SO:0001576	5_prime_UTR_truncation	SO:0001564
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	1641751	SO:0002014	SO:0001576	5_prime_UTR_elongation	SO:0001564
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	1641752	SO:0002015	SO:0001576	3_prime_UTR_truncation	SO:0001564
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	1641753	SO:0002016	SO:0001576	3_prime_UTR_elongation	SO:0001564
5	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A transcript variant occurring within a conserved region of an intron." [SO:ke]	SO	1641754	SO:0002018	SO:0001878	conserved_intron_variant	SO:0001537
5	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	1641755	SO:0002019	SO:0001576	start_retained_variant	SO:0001564
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]	SO	1641756	SO:0002020	SO:0001411	boundary_element	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]	SO	1641757	SO:0002021	SO:0001411	mating_type_region_replication_fork_barrier	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	SO	1641758	SO:0002022	SO:0000831	priRNA	SO:0001411
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]	SO	1641759	SO:0002023	SO:0001409	multiplexing_sequence_identifier	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1641760	SO:0002024	SO:0001683	W_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	2082424	SO:0002024	SO:0001411	W_region	SO:0000001
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	SO	1641762	SO:0002025	SO:0001411	cis_acting_homologous_chromosome_pairing_region	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]	SO	1641763	SO:0002027	SO:0000001	uORF	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]	SO	1641764	SO:0002028	SO:0000001	sORF	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]	SO	1641765	SO:0002029	SO:0000001	tnaORF	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	1641766	SO:0002030	SO:0001683	X_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	2082427	SO:0002030	SO:0001411	X_region	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	SO	1641768	SO:0002031	SO:0000831	shRNA	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	1641769	SO:0005837	SO:0000673	U14_snoRNA_primary_transcript	SO:0000831
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	1641770	SO:0005841	SO:0000233	methylation_guide_snoRNA	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	SO	1641771	SO:0005843	SO:0000831	rRNA_cleavage_RNA	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	1641772	SO:0005845	SO:0000831	exon_of_single_exon_gene	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An exon that is the only exon in a gene." [RSC:cb]	SO	2165204	SO:0005845	SO:0000001	exon_of_single_exon_gene	SO:0000110
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"" []	SO	1641774	SO:0005847	SO:0000733	cassette_array_member	SO:0000400
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2486380	SO:0005850	SO:0000001	primer_binding_site	SO:0000110
5	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	1641776	SO:0005850	SO:0001039	primer_binding_site	SO:0001037
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	1641777	SO:0005856	SO:0000673	selenocysteine_tRNA_primary_transcript	SO:0000831
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	1641778	SO:0005857	SO:0000673	selenocysteinyl_tRNA	SO:0000831
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	1641779	SO:0100001	SO:0000104	biochemical_region_of_peptide	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	2082438	SO:0100001	SO:0001411	biochemical_region_of_peptide	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	1641781	SO:0100002	SO:0000839	molecular_contact_region	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	1641782	SO:0100002	SO:0000839	molecular_contact_region	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]	SO	1805777	SO:0100003	SO:0000001	intrinsically_unstructured_polypeptide_region	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1641785	SO:0100004	SO:0000104	catmat_left_handed_three	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2082442	SO:0100004	SO:0001411	catmat_left_handed_three	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1641787	SO:0100005	SO:0000104	catmat_left_handed_four	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2082444	SO:0100005	SO:0001411	catmat_left_handed_four	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1641789	SO:0100006	SO:0000104	catmat_right_handed_three	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2082446	SO:0100006	SO:0001411	catmat_right_handed_three	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1641791	SO:0100007	SO:0000104	catmat_right_handed_four	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2082448	SO:0100007	SO:0001411	catmat_right_handed_four	SO:0000001
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	1641793	SO:0100008	SO:0000104	alpha_beta_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2082450	SO:0100008	SO:0001411	alpha_beta_motif	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]	SO	2165205	SO:0100009	SO:0000001	lipoprotein_signal_peptide	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]	SO	1641796	SO:0100010	SO:0000001	no_output	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	1641797	SO:0100012	SO:0000104	peptide_coil	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	2082452	SO:0100012	SO:0001411	peptide_coil	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]	SO	2731433	SO:0100014	SO:0000001	n_terminal_region	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]	SO	2731434	SO:0100015	SO:0000001	c_terminal_region	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]	SO	2731435	SO:0100016	SO:0000001	central_hydrophobic_region_of_signal_peptide	SO:0000110
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	1641802	SO:0100017	SO:0000104	polypeptide_conserved_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	2082454	SO:0100017	SO:0001411	polypeptide_conserved_motif	SO:0000001
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	1641804	SO:0100018	SO:0000839	polypeptide_binding_motif	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	1641805	SO:0100018	SO:0000839	polypeptide_binding_motif	SO:0001411
5	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	1641806	SO:0100019	SO:0000839	polypeptide_catalytic_motif	SO:0000104
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	1641807	SO:0100019	SO:0000839	polypeptide_catalytic_motif	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	2707065	SO:0100020	SO:0001411	polypeptide_DNA_contact	SO:0000001
5	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	1641809	SO:0100020	SO:0100021	polypeptide_DNA_contact	SO:0000839
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]	SO	1641810	SO:1000008	SO:0000001	point_mutation	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1641811	SO:1000009	SO:0000001	transition	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	1641812	SO:1000010	SO:0001059	pyrimidine_transition	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	1641813	SO:1000010	SO:0001411	pyrimidine_transition	SO:0000001
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	1641814	SO:1000011	SO:1000002	C_to_T_transition	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	1641815	SO:1000011	SO:1000002	C_to_T_transition	SO:0001411
5	"A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]	\N	substitution	SOFA	SOFA	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1641816	SO:1000012	SO:0001483	C_to_T_transition_at_pCpG_site	SO:1000002
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"" []	SO	1641817	SO:1000013	SO:1000002	T_to_C_transition	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1641818	SO:1000013	SO:1000002	T_to_C_transition	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	1641819	SO:1000014	SO:0001059	purine_transition	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	1641820	SO:1000014	SO:0001411	purine_transition	SO:0000001
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	1641821	SO:1000015	SO:1000002	A_to_G_transition	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	1641822	SO:1000015	SO:1000002	A_to_G_transition	SO:0001411
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	1641823	SO:1000016	SO:1000002	G_to_A_transition	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	1641824	SO:1000016	SO:1000002	G_to_A_transition	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	1641825	SO:1000017	SO:0000001	transversion	SO:0000110
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	1641826	SO:1000018	SO:0001059	pyrimidine_to_purine_transversion	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	1641827	SO:1000018	SO:0001411	pyrimidine_to_purine_transversion	SO:0000001
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	1641828	SO:1000019	SO:1000002	C_to_A_transversion	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	1641829	SO:1000019	SO:1000002	C_to_A_transversion	SO:0001411
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"" []	SO	1641830	SO:1000020	SO:1000002	C_to_G_transversion	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	1641831	SO:1000020	SO:1000002	C_to_G_transversion	SO:0001411
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transversion from T to A." [SO:ke]	SO	1641832	SO:1000021	SO:1000002	T_to_A_transversion	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transversion from T to A." [SO:ke]	SO	1641833	SO:1000021	SO:1000002	T_to_A_transversion	SO:0001411
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transversion from T to G." [SO:ke]	SO	1641834	SO:1000022	SO:1000002	T_to_G_transversion	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transversion from T to G." [SO:ke]	SO	1641835	SO:1000022	SO:1000002	T_to_G_transversion	SO:0001411
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	1641836	SO:1000023	SO:0001059	purine_to_pyrimidine_transversion	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	1641837	SO:1000023	SO:0001411	purine_to_pyrimidine_transversion	SO:0000001
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	1641838	SO:1000024	SO:1000002	A_to_C_transversion	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	1641839	SO:1000024	SO:1000002	A_to_C_transversion	SO:0001411
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	1641840	SO:1000025	SO:1000002	A_to_T_transversion	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	1641841	SO:1000025	SO:1000002	A_to_T_transversion	SO:0001411
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	1641842	SO:1000026	SO:1000002	G_to_C_transversion	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	1641843	SO:1000026	SO:1000002	G_to_C_transversion	SO:0001411
5	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	1641844	SO:1000027	SO:1000002	G_to_T_transversion	SO:0001059
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	1641845	SO:1000027	SO:1000002	G_to_T_transversion	SO:0001411
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	1641846	SO:1000028	SO:0001506	intrachromosomal_mutation	SO:0001026
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	1641847	SO:1000029	SO:0001507	chromosomal_deletion	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	1641848	SO:1000029	SO:0001524	chromosomal_deletion	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	1641849	SO:1000030	SO:0001507	chromosomal_inversion	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	1641850	SO:1000030	SO:0001524	chromosomal_inversion	SO:0001506
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	1641851	SO:1000031	SO:0001506	interchromosomal_mutation	SO:0001026
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	1641852	SO:1000037	SO:0001506	chromosomal_duplication	SO:0001026
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	1641853	SO:1000038	SO:0001507	intrachromosomal_duplication	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	1641854	SO:1000038	SO:0001524	intrachromosomal_duplication	SO:0001506
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	1641855	SO:1000039	SO:0001059	direct_tandem_duplication	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	1641856	SO:1000039	SO:0001411	direct_tandem_duplication	SO:0000001
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	1641857	SO:1000040	SO:0001059	inverted_tandem_duplication	SO:0000110
5	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	1641858	SO:1000040	SO:0001411	inverted_tandem_duplication	SO:0000001
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	1805783	SO:1000041	SO:0001507	intrachromosomal_transposition	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	1805784	SO:1000041	SO:0001524	intrachromosomal_transposition	SO:0001506
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	1641861	SO:1000042	SO:0001506	compound_chromosome	SO:0001026
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	1641862	SO:1000043	SO:0000240	Robertsonian_fusion	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	1641863	SO:1000043	SO:0000240	Robertsonian_fusion	SO:0001524
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	1641864	SO:1000044	SO:0001507	chromosomal_translocation	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	1641865	SO:1000044	SO:0001524	chromosomal_translocation	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	1641866	SO:1000045	SO:0001507	ring_chromosome	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	1641867	SO:1000045	SO:0001524	ring_chromosome	SO:0001506
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	1641868	SO:1000046	SO:0000240	pericentric_inversion	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	1641869	SO:1000046	SO:0000240	pericentric_inversion	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	1641870	SO:1000047	SO:0000240	paracentric_inversion	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	1641871	SO:1000047	SO:0000240	paracentric_inversion	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	1641872	SO:1000048	SO:0000240	reciprocal_chromosomal_translocation	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	1641873	SO:1000048	SO:0000240	reciprocal_chromosomal_translocation	SO:0001524
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	1641874	SO:1000136	SO:0001506	autosynaptic_chromosome	SO:0001026
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	1641875	SO:1000138	SO:0001507	homo_compound_chromosome	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	1641876	SO:1000138	SO:0001524	homo_compound_chromosome	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	1641877	SO:1000140	SO:0001507	hetero_compound_chromosome	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	1641878	SO:1000140	SO:0001524	hetero_compound_chromosome	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	1641879	SO:1000141	SO:0001507	chromosome_fission	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	1641880	SO:1000141	SO:0001524	chromosome_fission	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	1641881	SO:1000142	SO:0001507	dexstrosynaptic_chromosome	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	1641882	SO:1000142	SO:0001524	dexstrosynaptic_chromosome	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	1641883	SO:1000143	SO:0001507	laevosynaptic_chromosome	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	1641884	SO:1000143	SO:0001524	laevosynaptic_chromosome	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	1641885	SO:1000144	SO:0001507	free_duplication	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	1641886	SO:1000144	SO:0001524	free_duplication	SO:0001506
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	1641887	SO:1000145	SO:0000240	free_ring_duplication	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	1641888	SO:1000145	SO:0000240	free_ring_duplication	SO:0001524
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	1641889	SO:1000146	SO:0001506	complex_chromosomal_mutation	SO:0001026
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	1641890	SO:1000147	SO:0000240	deficient_translocation	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	1641891	SO:1000147	SO:0000240	deficient_translocation	SO:0001524
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	1805785	SO:1000148	SO:0001507	inversion_cum_translocation	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	1805786	SO:1000148	SO:0001524	inversion_cum_translocation	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	1805787	SO:1000149	SO:0001507	bipartite_duplication	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	1805788	SO:1000149	SO:0001524	bipartite_duplication	SO:0001506
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	1641896	SO:1000150	SO:0000240	cyclic_translocation	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	1641897	SO:1000150	SO:0000240	cyclic_translocation	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	1641898	SO:1000151	SO:0000240	bipartite_inversion	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	1641899	SO:1000151	SO:0000240	bipartite_inversion	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1641900	SO:1000152	SO:0000240	uninverted_insertional_duplication	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1641901	SO:1000152	SO:0000240	uninverted_insertional_duplication	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1641902	SO:1000153	SO:0000240	inverted_insertional_duplication	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1641903	SO:1000153	SO:0000240	inverted_insertional_duplication	SO:0001524
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	1641904	SO:1000154	SO:0001507	insertional_duplication	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	1641905	SO:1000154	SO:0001524	insertional_duplication	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	1641906	SO:1000155	SO:0001507	interchromosomal_transposition	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	1641907	SO:1000155	SO:0001524	interchromosomal_transposition	SO:0001506
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	1641908	SO:1000156	SO:0000240	inverted_interchromosomal_transposition	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	1641909	SO:1000156	SO:0000240	inverted_interchromosomal_transposition	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1641910	SO:1000157	SO:0000240	uninverted_interchromosomal_transposition	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1641911	SO:1000157	SO:0000240	uninverted_interchromosomal_transposition	SO:0001524
6	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1805789	SO:1000158	SO:0000240	inverted_intrachromosomal_transposition	SO:0001507
6	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	1805790	SO:1000158	SO:0000240	inverted_intrachromosomal_transposition	SO:0001524
6	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1805791	SO:1000159	SO:0000240	uninverted_intrachromosomal_transposition	SO:0001507
6	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	1805792	SO:1000159	SO:0000240	uninverted_intrachromosomal_transposition	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1641916	SO:1000160	SO:0000240	unoriented_insertional_duplication	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1641917	SO:1000160	SO:0000240	unoriented_insertional_duplication	SO:0001524
5	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1641918	SO:1000161	SO:0000240	unoriented_interchromosomal_transposition	SO:0001507
5	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1641919	SO:1000161	SO:0000240	unoriented_interchromosomal_transposition	SO:0001524
6	"A collection of one or more sequences of an individual." [SO:ke]	\N	variant_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1805793	SO:1000162	SO:0000240	unoriented_intrachromosomal_transposition	SO:0001507
6	"" []	\N	chromosomally_aberrant_genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	1805794	SO:1000162	SO:0000240	unoriented_intrachromosomal_transposition	SO:0001524
5	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"" []	SO	1641922	SO:1000170	SO:0001506	uncharacterised_chromosomal_mutation	SO:0001026
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	1805795	SO:1000171	SO:0001507	deficient_inversion	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	1805796	SO:1000171	SO:0001524	deficient_inversion	SO:0001506
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	DBVAR	sequence_feature	SOFA	SOFA	sequence	"A duplication consisting of 2 identical adjacent regions." [SO:ke]	SO	1641925	SO:1000173	SO:0000001	tandem_duplication	SO:0000110
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	1641926	SO:1000175	SO:0001507	partially_characterised_chromosomal_mutation	SO:0001260
5	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"" []	SO	1641927	SO:1000175	SO:0001524	partially_characterised_chromosomal_mutation	SO:0001506
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	1641928	SO:1000182	SO:0001026	chromosome_number_variation	SO:0001260
5	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	1641929	SO:1000183	SO:0001026	chromosome_structure_variation	SO:0001260
5	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is alternatively spliced." [SO:xp]	SO	1641930	SO:1001187	SO:0000001	alternatively_spliced_transcript	SO:0000110
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]	SO	1641931	SO:1001190	SO:0000401	encodes_different_polypeptides_different_stop	SO:0000733
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]	SO	1641932	SO:1001191	SO:0000401	encodes_overlapping_peptides_different_start	SO:0000733
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]	SO	1641933	SO:1001192	SO:0000733	encodes_disjoint_polypeptides	SO:0000400
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]	SO	1641934	SO:1001193	SO:0000401	encodes_overlapping_polypeptides_different_start_and_stop	SO:0000733
5	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]	SO	1641935	SO:1001195	SO:0000733	encodes_overlapping_peptides	SO:0000400
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]	SO	2165209	SO:1001196	SO:0000001	cryptogene	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	1805798	SO:1001197	SO:0001411	dicistronic_primary_transcript	SO:0000001
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	1641940	SO:1001246	SO:0000233	CDS_independently_known	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	1641941	SO:1001246	SO:0000833	CDS_independently_known	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	1641942	SO:1001246	SO:0000833	CDS_independently_known	SO:0001411
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	1641943	SO:1001247	SO:0000234	orphan_CDS	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	1641944	SO:1001247	SO:0000834	orphan_CDS	SO:0000833
6	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	1805799	SO:1001249	SO:0000234	CDS_supported_by_domain_match_data	SO:0000233
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	1805800	SO:1001249	SO:0000834	CDS_supported_by_domain_match_data	SO:0000833
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	1805801	SO:1001251	SO:0000233	CDS_supported_by_sequence_similarity_data	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	1805802	SO:1001251	SO:0000833	CDS_supported_by_sequence_similarity_data	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	1805803	SO:1001251	SO:0000833	CDS_supported_by_sequence_similarity_data	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	1641950	SO:1001254	SO:0000233	CDS_predicted	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	1641951	SO:1001254	SO:0000833	CDS_predicted	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	1641952	SO:1001254	SO:0000833	CDS_predicted	SO:0001411
6	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	1805804	SO:1001259	SO:0000234	CDS_supported_by_EST_or_cDNA_data	SO:0000233
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	1805805	SO:1001259	SO:0000834	CDS_supported_by_EST_or_cDNA_data	SO:0000833
5	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	1641955	SO:1001260	SO:0000203	internal_Shine_Dalgarno_sequence	SO:0000836
8	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2486387	SO:1001260	SO:0000233	internal_Shine_Dalgarno_sequence	SO:0000673
8	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2486388	SO:1001260	SO:0000833	internal_Shine_Dalgarno_sequence	SO:0000673
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2486389	SO:1001260	SO:0000833	internal_Shine_Dalgarno_sequence	SO:0001411
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	1641959	SO:1001261	SO:0000831	recoded_mRNA	SO:0001411
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a translational frameshift of -1." [SO:ke]	SO	1641960	SO:1001262	SO:0000237	minus_1_translationally_frameshifted	SO:0000733
5	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing a translational frameshift of +1." [SO:ke]	SO	1641961	SO:1001263	SO:0000237	plus_1_translationally_frameshifted	SO:0000733
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	1805809	SO:1001264	SO:0000831	mRNA_recoded_by_translational_bypass	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	1805810	SO:1001265	SO:0000831	mRNA_recoded_by_codon_redefinition	SO:0001411
5	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	1641964	SO:1001268	SO:0000673	recoding_stimulatory_region	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	2442067	SO:1001268	SO:0001411	recoding_stimulatory_region	SO:0000001
5	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	1641966	SO:1001269	SO:0000851	four_bp_start_codon	SO:0000316
5	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	1641967	SO:1001269	SO:0000851	four_bp_start_codon	SO:0000836
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	1641968	SO:1001271	SO:0000185	archaeal_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	1641969	SO:1001271	SO:0000833	archaeal_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	1641970	SO:1001271	SO:0000833	archaeal_intron	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1641971	SO:1001272	SO:0000185	tRNA_intron	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1641972	SO:1001272	SO:0000833	tRNA_intron	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	1641973	SO:1001272	SO:0000833	tRNA_intron	SO:0001411
5	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	\N	CDS	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	1641974	SO:1001273	SO:0000851	CTG_start_codon	SO:0000316
5	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	1641975	SO:1001273	SO:0000851	CTG_start_codon	SO:0000836
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	1641976	SO:1001274	SO:0000233	SECIS_element	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	1641977	SO:1001274	SO:0000833	SECIS_element	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	1641978	SO:1001274	SO:0000833	SECIS_element	SO:0001411
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	1641979	SO:1001277	SO:0000233	three_prime_recoding_site	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	1641980	SO:1001277	SO:0000833	three_prime_recoding_site	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	1641981	SO:1001277	SO:0000833	three_prime_recoding_site	SO:0001411
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	1641982	SO:1001279	SO:0000234	three_prime_stem_loop_structure	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	1641983	SO:1001279	SO:0000834	three_prime_stem_loop_structure	SO:0000833
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	1641984	SO:1001280	SO:0000233	five_prime_recoding_site	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	1641985	SO:1001280	SO:0000833	five_prime_recoding_site	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	1641986	SO:1001280	SO:0000833	five_prime_recoding_site	SO:0001411
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	1641987	SO:1001281	SO:0000234	flanking_three_prime_quadruplet_recoding_signal	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	1641988	SO:1001281	SO:0000834	flanking_three_prime_quadruplet_recoding_signal	SO:0000833
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	1641989	SO:1001282	SO:0000234	UAG_stop_codon_signal	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	1641990	SO:1001282	SO:0000834	UAG_stop_codon_signal	SO:0000833
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	1641991	SO:1001283	SO:0000234	UAA_stop_codon_signal	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	1641992	SO:1001283	SO:0000834	UAA_stop_codon_signal	SO:0000833
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	1641993	SO:1001285	SO:0000234	UGA_stop_codon_signal	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	1641994	SO:1001285	SO:0000834	UGA_stop_codon_signal	SO:0000833
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	1641995	SO:1001286	SO:0000234	three_prime_repeat_recoding_signal	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	1641996	SO:1001286	SO:0000834	three_prime_repeat_recoding_signal	SO:0000833
5	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	1641997	SO:1001287	SO:0000234	distant_three_prime_recoding_signal	SO:0000233
5	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	1641998	SO:1001287	SO:0000834	distant_three_prime_recoding_signal	SO:0000833
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	1641999	SO:1001288	SO:0000233	stop_codon_signal	SO:0000673
5	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	1642000	SO:1001288	SO:0000833	stop_codon_signal	SO:0000673
5	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	1642001	SO:1001288	SO:0000833	stop_codon_signal	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"" []	SO	2080910	SO:0000004	SO:0000831	interior_coding_exon	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2548755	SO:0000004	SO:0000001	interior_coding_exon	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	SO	2080912	SO:0000012	SO:0001411	scRNA_primary_transcript	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SO	2080913	SO:0000013	SO:0001411	scRNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	2080914	SO:0000014	SO:0001683	INR_motif	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	2080915	SO:0000014	SO:0001055	INR_motif	SO:0001679
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	2080916	SO:0000015	SO:0001683	DPE_motif	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	2080917	SO:0000015	SO:0001055	DPE_motif	SO:0001679
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	2080918	SO:0000016	SO:0001683	BREu_motif	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	2080919	SO:0000016	SO:0001055	BREu_motif	SO:0001679
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	2548756	SO:0000017	SO:0000001	PSE_motif	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]	SO	2080921	SO:0000017	SO:0000831	PSE_motif	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]	SO	2080922	SO:0000020	SO:0000001	RNA_internal_loop	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	SO	2080923	SO:0000021	SO:0001411	asymmetric_RNA_internal_loop	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]	SO	2080924	SO:0000022	SO:0000001	A_minor_RNA_motif	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	2080925	SO:0000023	SO:0001683	K_turn_RNA_motif	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	2080926	SO:0000024	SO:0001683	sarcin_like_RNA_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	SO	2080927	SO:0000025	SO:0001411	symmetric_RNA_internal_loop	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2080928	SO:0000026	SO:0000001	RNA_junction_loop	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2080929	SO:0000027	SO:0001411	RNA_hook_turn	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]	SO	2080930	SO:0000032	SO:0000001	DNA_aptamer	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]	SO	2080931	SO:0000033	SO:0000001	RNA_aptamer	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]	SO	2080932	SO:0000034	SO:0000001	morpholino_oligo	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]	SO	2548757	SO:0000035	SO:0000001	riboswitch	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	2080936	SO:0000037	SO:0000831	locus_control_region	SO:0001411
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]	SO	2080937	SO:0000054	SO:0001026	aneuploid	SO:0001260
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	2080938	SO:0000055	SO:0001506	hyperploid	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	2080939	SO:0000056	SO:0001506	hypoploid	SO:0001026
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SO	2080940	SO:0000057	SO:0001411	operator	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]	SO	2080941	SO:0000059	SO:0000001	nuclease_binding_site	SO:0000110
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"" []	SO	2080942	SO:0000060	SO:0001506	compound_chromosome_arm	SO:0001026
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	SO	2080943	SO:0000061	SO:0001411	restriction_enzyme_binding_site	SO:0000001
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	2279361	SO:0000062	SO:0001507	deficient_intrachromosomal_transposition	SO:0001260
7	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	2279362	SO:0000062	SO:0001524	deficient_intrachromosomal_transposition	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	2080946	SO:0000063	SO:0001507	deficient_interchromosomal_transposition	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	2080947	SO:0000063	SO:0001524	deficient_interchromosomal_transposition	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]	SO	2080948	SO:0000065	SO:0001026	free_chromosome_arm	SO:0001260
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]	SO	2080949	SO:0000070	SO:0000733	inside_intron_antiparallel	SO:0000400
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]	SO	2080950	SO:0000071	SO:0000733	inside_intron_parallel	SO:0000400
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2080951	SO:0000107	SO:0001409	sequencing_primer	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA with a frameshift." [SO:xp]	SO	2080952	SO:0000108	SO:0001411	mRNA_with_frameshift	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]	SO	2080953	SO:0000112	SO:0000001	primer	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A methylated deoxy-cytosine." [SO:ke]	SO	2080954	SO:0000114	SO:0000001	methylated_cytosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]	SO	2080955	SO:0000120	SO:0000001	protein_coding_primary_transcript	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	2080956	SO:0000121	SO:0001409	forward_primer	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	2080957	SO:0000132	SO:0001409	reverse_primer	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	2548758	SO:0000139	SO:0000831	ribosome_entry_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Region in mRNA where ribosome assembles." [SO:ke]	SO	2917071	SO:0000139	SO:0000001	ribosome_entry_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]	SO	2279363	SO:0000140	SO:0000001	attenuator	SO:0000110
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	2279364	SO:0000145	SO:0000233	recoded_codon	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	2279365	SO:0000145	SO:0000833	recoded_codon	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	2279366	SO:0000145	SO:0000833	recoded_codon	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]	SO	2279367	SO:0000148	SO:0000001	supercontig	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A modified  base in which adenine has been methylated." [SO:ke]	SO	2080971	SO:0000161	SO:0000001	methylated_adenine	SO:0000110
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	2080973	SO:0000163	SO:0000673	five_prime_cis_splice_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	2706462	SO:0000163	SO:0001411	five_prime_cis_splice_site	SO:0000001
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	2080975	SO:0000164	SO:0000673	three_prime_cis_splice_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	2706463	SO:0000164	SO:0001411	three_prime_cis_splice_site	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2080977	SO:0000165	SO:0000831	enhancer	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An enhancer bound by a factor." [SO:xp]	SO	2080978	SO:0000166	SO:0005836	enhancer_bound_by_factor	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SO	2080979	SO:0000167	SO:0001411	promoter	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	2080980	SO:0000169	SO:0005836	RNApol_I_promoter	SO:0000831
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	2080981	SO:0000170	SO:0005836	RNApol_II_promoter	SO:0000831
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	2080982	SO:0000171	SO:0005836	RNApol_III_promoter	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2917072	SO:0000172	SO:0000001	CAAT_signal	SO:0000110
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2080984	SO:0000172	SO:0001679	CAAT_signal	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2885615	SO:0000173	SO:0001411	GC_rich_promoter_region	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2080986	SO:0000173	SO:0001679	GC_rich_promoter_region	SO:0005836
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	2080987	SO:0000174	SO:0001683	TATA_box	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	3011584	SO:0000175	SO:0000001	minus_10_signal	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2548760	SO:0000175	SO:0005836	minus_10_signal	SO:0000831
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2080990	SO:0000175	SO:0001055	minus_10_signal	SO:0001679
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	3011585	SO:0000176	SO:0000001	minus_35_signal	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2548761	SO:0000176	SO:0005836	minus_35_signal	SO:0000831
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2080993	SO:0000176	SO:0001055	minus_35_signal	SO:0001679
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	2080996	SO:0000184	SO:0000673	U2_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	2706474	SO:0000184	SO:0001411	U2_intron	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	2441061	SO:0000186	SO:0000001	LTR_retrotransposon	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A retrotransposon flanked by long terminal repeat sequences." [SO:ke]	SO	2080999	SO:0000186	SO:0001411	LTR_retrotransposon	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	2441062	SO:0000189	SO:0000001	non_LTR_retrotransposon	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A retrotransposon without long terminal repeat sequences." [SO:ke]	SO	2081002	SO:0000189	SO:0001411	non_LTR_retrotransposon	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081003	SO:0000190	SO:0000831	five_prime_intron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2548762	SO:0000190	SO:0000001	five_prime_intron	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081005	SO:0000191	SO:0000831	interior_intron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2548763	SO:0000191	SO:0000001	interior_intron	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081007	SO:0000192	SO:0000831	three_prime_intron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2548764	SO:0000192	SO:0000001	three_prime_intron	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	2081009	SO:0000194	SO:0001037	LINE_element	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	2081010	SO:0000194	SO:0001037	LINE_element	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	2279368	SO:0000196	SO:0000831	five_prime_coding_exon_coding_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]	SO	2764348	SO:0000196	SO:0000001	five_prime_coding_exon_coding_region	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	2279370	SO:0000197	SO:0000831	three_prime_coding_exon_coding_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]	SO	2764349	SO:0000197	SO:0000001	three_prime_coding_exon_coding_region	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	2081017	SO:0000200	SO:0000831	five_prime_coding_exon	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The 5' most coding exon." [SO:ke]	SO	2548767	SO:0000200	SO:0000001	five_prime_coding_exon	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	2081020	SO:0000202	SO:0000831	three_prime_coding_exon	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The coding exon that is most 3-prime on a given transcript." [SO:ma]	SO	2548768	SO:0000202	SO:0000001	three_prime_coding_exon	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	2081022	SO:0000203	SO:0000831	UTR	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]	SO	2548769	SO:0000203	SO:0000001	UTR	SO:0000110
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081024	SO:0000204	SO:0000673	five_prime_UTR	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2706476	SO:0000204	SO:0001411	five_prime_UTR	SO:0000001
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081026	SO:0000205	SO:0000673	three_prime_UTR	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2706477	SO:0000205	SO:0001411	three_prime_UTR	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	2081028	SO:0000206	SO:0001037	SINE_element	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	2081029	SO:0000206	SO:0001037	SINE_element	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	2441079	SO:0000208	SO:0000001	terminal_inverted_repeat_element	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	2081031	SO:0000208	SO:0001411	terminal_inverted_repeat_element	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SO	2081032	SO:0000209	SO:0001411	rRNA_primary_transcript	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	SO	2081033	SO:0000210	SO:0001411	tRNA_primary_transcript	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	2081034	SO:0000211	SO:0000831	alanine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	2081035	SO:0000212	SO:0000831	arginine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	2081036	SO:0000213	SO:0000831	asparagine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	2081037	SO:0000214	SO:0000831	aspartic_acid_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	2081038	SO:0000215	SO:0000831	cysteine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	2081039	SO:0000216	SO:0000831	glutamic_acid_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	2081040	SO:0000217	SO:0000831	glutamine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	2081041	SO:0000218	SO:0000831	glycine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	2081042	SO:0000219	SO:0000831	histidine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	2081043	SO:0000220	SO:0000831	isoleucine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	2081044	SO:0000221	SO:0000831	leucine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	2081045	SO:0000222	SO:0000831	lysine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	2081046	SO:0000223	SO:0000831	methionine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	2081047	SO:0000224	SO:0000831	phenylalanine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	2081048	SO:0000225	SO:0000831	proline_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	2081049	SO:0000226	SO:0000831	serine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	2081050	SO:0000227	SO:0000831	threonine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	2081051	SO:0000228	SO:0000831	tryptophan_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	2081052	SO:0000229	SO:0000831	tyrosine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	2081053	SO:0000230	SO:0000831	valine_tRNA_primary_transcript	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	SO	2081054	SO:0000231	SO:0001411	snRNA_primary_transcript	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	SO	2081055	SO:0000232	SO:0001411	snoRNA_primary_transcript	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	SO	2081056	SO:0000234	SO:0000001	mRNA	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]	SO	2081057	SO:0000235	SO:0000001	TF_binding_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	2441104	SO:0000238	SO:0000001	foldback_element	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	SO	2081059	SO:0000238	SO:0001411	foldback_element	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	2081060	SO:0000241	SO:0000673	internal_UTR	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	2706499	SO:0000241	SO:0001411	internal_UTR	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	2081062	SO:0000242	SO:0000673	untranslated_region_polycistronic_mRNA	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	2706500	SO:0000242	SO:0001411	untranslated_region_polycistronic_mRNA	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	2548770	SO:0000243	SO:0000673	internal_ribosome_entry_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	2961203	SO:0000243	SO:0001411	internal_ribosome_entry_site	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SO	2081066	SO:0000252	SO:0001411	rRNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SO	2081067	SO:0000253	SO:0001411	tRNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	2081068	SO:0000254	SO:0000831	alanyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	2081069	SO:0000255	SO:0000831	rRNA_small_subunit_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	2081070	SO:0000256	SO:0000831	asparaginyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	2081071	SO:0000257	SO:0000831	aspartyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	2081072	SO:0000258	SO:0000831	cysteinyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	2081073	SO:0000259	SO:0000831	glutaminyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	2081074	SO:0000260	SO:0000831	glutamyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	2081075	SO:0000261	SO:0000831	glycyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	2081076	SO:0000262	SO:0000831	histidyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	2081077	SO:0000263	SO:0000831	isoleucyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	2081078	SO:0000264	SO:0000831	leucyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	2081079	SO:0000265	SO:0000831	lysyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	2081080	SO:0000266	SO:0000831	methionyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	2081081	SO:0000267	SO:0000831	phenylalanyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	2081082	SO:0000268	SO:0000831	prolyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	2081083	SO:0000269	SO:0000831	seryl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	2081084	SO:0000270	SO:0000831	threonyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	2081085	SO:0000271	SO:0000831	tryptophanyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	2081086	SO:0000272	SO:0000831	tyrosyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	2081087	SO:0000273	SO:0000831	valyl_tRNA	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SO	2081088	SO:0000274	SO:0001411	snRNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SO	2081089	SO:0000275	SO:0001411	snoRNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	2081090	SO:0000276	SO:0000831	miRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	2081091	SO:0000282	SO:0000831	mRNA_with_minus_1_frameshift	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081093	SO:0000286	SO:0001037	long_terminal_repeat	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081094	SO:0000286	SO:0001037	long_terminal_repeat	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	SO	2081095	SO:0000289	SO:0000001	microsatellite	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2081096	SO:0000290	SO:0001411	dinucleotide_repeat_microsatellite_feature	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2081097	SO:0000291	SO:0001411	trinucleotide_repeat_microsatellite_feature	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	2081098	SO:0000295	SO:0000673	U12_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	2706523	SO:0000295	SO:0001411	U12_intron	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2081100	SO:0000300	SO:0000001	recombination_feature_of_rearranged_gene	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2081101	SO:0000301	SO:0001411	vertebrate_immune_system_gene_recombination_feature	SO:0000001
6	"" []	\N	recombination_feature	\N	\N	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081102	SO:0000302	SO:0000669	J_gene_recombination_feature	SO:0000298
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	2081105	SO:0000316	SO:0000831	CDS	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]	SO	2548772	SO:0000316	SO:0000001	CDS	SO:0000110
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	2279372	SO:0000318	SO:0000233	start_codon	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	2279373	SO:0000318	SO:0000833	start_codon	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	2279374	SO:0000318	SO:0000833	start_codon	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	2279375	SO:0000319	SO:0000233	stop_codon	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	2279376	SO:0000319	SO:0000833	stop_codon	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	2279377	SO:0000319	SO:0000833	stop_codon	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	2548773	SO:0000320	SO:0000831	intronic_splice_enhancer	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Sequences within the intron that modulate splice site selection for some introns." [SO:ke]	SO	2917073	SO:0000320	SO:0000001	intronic_splice_enhancer	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	2081115	SO:0000321	SO:0000831	mRNA_with_plus_1_frameshift	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"" []	SO	2081116	SO:0000322	SO:0000409	nuclease_hypersensitive_site	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	2279378	SO:0000323	SO:0000673	coding_start	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	2848881	SO:0000323	SO:0001411	coding_start	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	2081119	SO:0000325	SO:0000831	rRNA_large_subunit_primary_transcript	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	SO	2081120	SO:0000326	SO:0000001	SAGE_tag	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	2279380	SO:0000327	SO:0000673	coding_end	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	2848882	SO:0000327	SO:0001411	coding_end	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2081123	SO:0000328	SO:0000001	microarray_oligo	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	2081124	SO:0000329	SO:0000831	mRNA_with_plus_2_frameshift	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]	SO	2081125	SO:0000331	SO:0000001	STS	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The boundary between two exons in a processed transcript." [SO:ke]	SO	2081126	SO:0000333	SO:0000001	exon_junction	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	2081127	SO:0000335	SO:0000831	mRNA_with_minus_2_frameshift	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]	SO	2081128	SO:0000337	SO:0000001	RNAi_reagent	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	2081129	SO:0000338	SO:0001037	MITE	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	2081130	SO:0000338	SO:0001037	MITE	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2081131	SO:0000342	SO:0000001	site_specific_recombination_target_region	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Region of a transcript that regulates splicing." [SO:ke]	SO	2081132	SO:0000344	SO:0001411	splice_enhancer	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]	SO	2081133	SO:0000345	SO:0000001	EST	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2081134	SO:0000346	SO:0000298	loxP_site	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	2081135	SO:0000350	SO:0000298	FRT_site	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	2081136	SO:0000354	SO:0000409	group_1_intron_homing_endonuclease_target_region	SO:0001411
7	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	2279382	SO:0000360	SO:0000673	codon	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	2848883	SO:0000360	SO:0001411	codon	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]	SO	2081139	SO:0000367	SO:0000298	attI_site	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SO	2081141	SO:0000370	SO:0001411	small_regulatory_ncRNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	2441169	SO:0000371	SO:0000001	conjugative_transposon	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	SO	2081143	SO:0000371	SO:0001411	conjugative_transposon	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An RNA with catalytic activity." [SO:ma]	SO	2081144	SO:0000374	SO:0000001	ribozyme	SO:0000110
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	2081145	SO:0000375	SO:0000673	rRNA_5_8S	SO:0000831
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	2081146	SO:0000376	SO:0000831	RNA_6S	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	2081147	SO:0000377	SO:0000831	CsrB_RsmB_RNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	2081148	SO:0000378	SO:0000831	DsrA_RNA	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	2081149	SO:0000379	SO:0000673	GcvB_RNA	SO:0000831
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]	SO	2081150	SO:0000380	SO:0000001	hammerhead_ribozyme	SO:0000110
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	2081151	SO:0000381	SO:0000185	group_IIA_intron	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	2081152	SO:0000381	SO:0000833	group_IIA_intron	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081153	SO:0000381	SO:0000833	group_IIA_intron	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	2081154	SO:0000382	SO:0000185	group_IIB_intron	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"" []	SO	2081155	SO:0000382	SO:0000833	group_IIB_intron	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081156	SO:0000382	SO:0000833	group_IIB_intron	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	2081157	SO:0000383	SO:0000831	MicF_RNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	2081158	SO:0000384	SO:0000831	OxyS_RNA	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SO	2081159	SO:0000385	SO:0001411	RNase_MRP_RNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SO	2081160	SO:0000386	SO:0001411	RNase_P_RNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	2081161	SO:0000387	SO:0000831	RprA_RNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	2081162	SO:0000388	SO:0000831	RRE_RNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	2081163	SO:0000389	SO:0000831	spot_42_RNA	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SO	2081164	SO:0000390	SO:0001411	telomerase_RNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	2081165	SO:0000391	SO:0000831	U1_snRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	2081166	SO:0000392	SO:0000831	U2_snRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	2081167	SO:0000393	SO:0000831	U4_snRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	2081168	SO:0000394	SO:0000831	U4atac_snRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	2081169	SO:0000395	SO:0000831	U5_snRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	2081170	SO:0000396	SO:0000831	U6_snRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	2081171	SO:0000397	SO:0000831	U6atac_snRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	2081172	SO:0000398	SO:0000831	U11_snRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	2081173	SO:0000399	SO:0000831	U12_snRNA	SO:0001411
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	2081174	SO:0000403	SO:0000673	U14_snoRNA	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SO	2081175	SO:0000404	SO:0001411	vault_RNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SO	2081176	SO:0000405	SO:0001411	Y_RNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	2081177	SO:0000406	SO:0000831	twintron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]	SO	2548776	SO:0000406	SO:0000001	twintron	SO:0000110
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	2081179	SO:0000407	SO:0000673	rRNA_18S	SO:0000831
6	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081180	SO:0000420	SO:0001039	five_prime_terminal_inverted_repeat	SO:0001037
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2764350	SO:0000420	SO:0000001	five_prime_terminal_inverted_repeat	SO:0000110
6	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081182	SO:0000421	SO:0001039	three_prime_terminal_inverted_repeat	SO:0001037
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2764351	SO:0000421	SO:0000001	three_prime_terminal_inverted_repeat	SO:0000110
6	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081184	SO:0000422	SO:0000101	U5_LTR_region	SO:0001039
6	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081186	SO:0000423	SO:0000101	R_LTR_region	SO:0001039
6	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081188	SO:0000424	SO:0000101	U3_LTR_region	SO:0001039
6	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081190	SO:0000425	SO:0001039	five_prime_LTR	SO:0001037
6	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081191	SO:0000426	SO:0001039	three_prime_LTR	SO:0001037
6	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	2081192	SO:0000427	SO:0000180	R_five_prime_LTR_region	SO:0000101
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2995344	SO:0000427	SO:0001411	R_five_prime_LTR_region	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	3023302	SO:0000427	SO:0000001	R_five_prime_LTR_region	SO:0000110
6	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	2081195	SO:0000428	SO:0000180	U5_five_prime_LTR_region	SO:0000101
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2995346	SO:0000428	SO:0001411	U5_five_prime_LTR_region	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	3023303	SO:0000428	SO:0000001	U5_five_prime_LTR_region	SO:0000110
6	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	2081198	SO:0000429	SO:0000180	U3_five_prime_LTR_region	SO:0000101
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2995348	SO:0000429	SO:0001411	U3_five_prime_LTR_region	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	3023304	SO:0000429	SO:0000001	U3_five_prime_LTR_region	SO:0000110
6	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	2081201	SO:0000430	SO:0000180	R_three_prime_LTR_region	SO:0000101
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2995350	SO:0000430	SO:0001411	R_three_prime_LTR_region	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	3023305	SO:0000430	SO:0000001	R_three_prime_LTR_region	SO:0000110
6	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	2081204	SO:0000431	SO:0000180	U3_three_prime_LTR_region	SO:0000101
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2995352	SO:0000431	SO:0001411	U3_three_prime_LTR_region	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	3023306	SO:0000431	SO:0000001	U3_three_prime_LTR_region	SO:0000110
6	"A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	\N	transposable_element	SOFA	\N	sequence	"" []	SO	2081207	SO:0000432	SO:0000180	U5_three_prime_LTR_region	SO:0000101
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2995354	SO:0000432	SO:0001411	U5_three_prime_LTR_region	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	3023307	SO:0000432	SO:0000001	U5_three_prime_LTR_region	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	2081210	SO:0000433	SO:0001037	non_LTR_retrotransposon_polymeric_tract	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]	SO	2081211	SO:0000433	SO:0001037	non_LTR_retrotransposon_polymeric_tract	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	2081212	SO:0000435	SO:0001037	RR_tract	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	2081213	SO:0000435	SO:0001037	RR_tract	SO:0001411
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	2081214	SO:0000439	SO:0001507	inverted_ring_chromosome	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"" []	SO	2081215	SO:0000439	SO:0001524	inverted_ring_chromosome	SO:0001506
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	2081216	SO:0000444	SO:0000831	three_prime_noncoding_exon	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Non-coding exon in the 3' UTR." [SO:ke]	SO	2548777	SO:0000444	SO:0000001	three_prime_noncoding_exon	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	2081218	SO:0000445	SO:0000831	five_prime_noncoding_exon	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Non-coding exon in the 5' UTR." [SO:ke]	SO	2548778	SO:0000445	SO:0000001	five_prime_noncoding_exon	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	2081220	SO:0000446	SO:0000831	UTR_intron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Intron located in the untranslated region." [SO:ke]	SO	2548779	SO:0000446	SO:0000001	UTR_intron	SO:0000110
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	2081222	SO:0000447	SO:0000673	five_prime_UTR_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	2706588	SO:0000447	SO:0001411	five_prime_UTR_intron	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	2081224	SO:0000448	SO:0000673	three_prime_UTR_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	2706589	SO:0000448	SO:0001411	three_prime_UTR_intron	SO:0000001
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]	SO	2081226	SO:0000453	SO:0001026	chromosomal_transposition	SO:0001260
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SO	2081227	SO:0000454	SO:0001411	rasiRNA	SO:0000001
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	2081228	SO:0000457	SO:0001506	interchromosomal_duplication	SO:0001026
6	"" []	\N	recombination_feature	\N	\N	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081229	SO:0000458	SO:0000669	D_gene_segment	SO:0000298
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2081230	SO:0000460	SO:0000298	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0001411
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	2081231	SO:0000461	SO:0001507	inversion_derived_bipartite_deficiency	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	2081232	SO:0000461	SO:0001524	inversion_derived_bipartite_deficiency	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	2081233	SO:0000465	SO:0001507	inversion_derived_deficiency_plus_duplication	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	2081234	SO:0000465	SO:0001524	inversion_derived_deficiency_plus_duplication	SO:0001506
6	"" []	\N	recombination_feature	\N	\N	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081235	SO:0000466	SO:0000669	V_gene_segment	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081236	SO:0000470	SO:0000669	J_gene_segment	SO:0000298
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]	SO	2081237	SO:0000473	SO:0000733	negatively_autoregulated	SO:0000400
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]	SO	2081238	SO:0000475	SO:0000733	positively_autoregulated	SO:0000400
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081242	SO:0000478	SO:0000669	C_gene_segment	SO:0000298
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	2081244	SO:0000481	SO:0001037	terminal_inverted_repeat	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]	SO	2081245	SO:0000481	SO:0001037	terminal_inverted_repeat	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2081246	SO:0000482	SO:0000298	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A primary transcript that is never translated into a protein." [SO:ke]	SO	2081247	SO:0000483	SO:0000001	nc_primary_transcript	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	2279385	SO:0000484	SO:0000831	three_prime_coding_exon_noncoding_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence of the 3' exon that is not coding." [SO:ke]	SO	2764353	SO:0000484	SO:0000001	three_prime_coding_exon_noncoding_region	SO:0000110
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081250	SO:0000485	SO:0000669	DJ_J_cluster	SO:0000298
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	2279387	SO:0000486	SO:0000831	five_prime_coding_exon_noncoding_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The sequence of the 5' exon preceding the start codon." [SO:ke]	SO	2764354	SO:0000486	SO:0000001	five_prime_coding_exon_noncoding_region	SO:0000110
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081253	SO:0000487	SO:0000669	VDJ_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081254	SO:0000488	SO:0000669	VDJ_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081255	SO:0000489	SO:0000669	VJ_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081256	SO:0000490	SO:0000669	VJ_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081257	SO:0000491	SO:0000669	VJ_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	2081258	SO:0000492	SO:0000669	D_gene_recombination_feature	SO:0000298
7	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2279389	SO:0000493	SO:0000299	three_prime_D_heptamer	SO:0000669
7	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2279390	SO:0000494	SO:0000299	three_prime_D_nonamer	SO:0000669
8	"" []	\N	recombination_feature	\N	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2548783	SO:0000495	SO:0000669	three_prime_D_spacer	SO:0000298
7	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2279391	SO:0000496	SO:0000299	five_prime_D_heptamer	SO:0000669
7	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2279392	SO:0000497	SO:0000299	five_prime_D_nonamer	SO:0000669
8	"" []	\N	recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2548784	SO:0000498	SO:0000669	five_prime_D_spacer	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081265	SO:0000504	SO:0000669	D_DJ_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081266	SO:0000505	SO:0000669	D_DJ_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081267	SO:0000506	SO:0000669	D_DJ_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081268	SO:0000508	SO:0000669	D_DJ_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081269	SO:0000509	SO:0000669	D_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081270	SO:0000510	SO:0000669	VD_gene_segment	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081271	SO:0000511	SO:0000669	J_C_cluster	SO:0000298
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	2081272	SO:0000512	SO:0001507	inversion_derived_deficiency_plus_aneuploid	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	2081273	SO:0000512	SO:0001524	inversion_derived_deficiency_plus_aneuploid	SO:0001506
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081274	SO:0000513	SO:0000669	J_cluster	SO:0000298
6	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081275	SO:0000514	SO:0000299	J_nonamer	SO:0000669
6	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081276	SO:0000515	SO:0000299	J_heptamer	SO:0000669
7	"" []	\N	recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2279393	SO:0000517	SO:0000669	J_spacer	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081278	SO:0000518	SO:0000669	V_DJ_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081279	SO:0000519	SO:0000669	V_DJ_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081280	SO:0000520	SO:0000669	V_VDJ_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081281	SO:0000521	SO:0000669	V_VDJ_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081282	SO:0000522	SO:0000669	V_VDJ_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081283	SO:0000523	SO:0000669	V_VJ_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081284	SO:0000524	SO:0000669	V_VJ_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081285	SO:0000525	SO:0000669	V_VJ_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081286	SO:0000526	SO:0000669	V_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081287	SO:0000527	SO:0000669	V_D_DJ_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081288	SO:0000528	SO:0000669	V_D_DJ_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081289	SO:0000529	SO:0000669	V_D_DJ_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081290	SO:0000530	SO:0000669	V_D_DJ_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081291	SO:0000531	SO:0000669	V_D_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081292	SO:0000532	SO:0000669	V_D_J_cluster	SO:0000298
6	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081293	SO:0000533	SO:0000299	V_heptamer	SO:0000669
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081294	SO:0000534	SO:0000669	V_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081295	SO:0000535	SO:0000669	V_J_C_cluster	SO:0000298
6	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081296	SO:0000536	SO:0000299	V_nonamer	SO:0000669
7	"" []	\N	recombination_feature	\N	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2279394	SO:0000537	SO:0000669	V_spacer	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081298	SO:0000538	SO:0000669	V_gene_recombination_feature	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081299	SO:0000539	SO:0000669	DJ_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081300	SO:0000540	SO:0000669	DJ_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081301	SO:0000541	SO:0000669	VDJ_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081302	SO:0000542	SO:0000669	V_DJ_C_cluster	SO:0000298
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	2441300	SO:0000544	SO:0000001	helitron	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]	SO	2081304	SO:0000544	SO:0001411	helitron	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	2081305	SO:0000545	SO:0000673	recoding_pseudoknot	SO:0000831
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	2081307	SO:0000547	SO:0001507	inversion_derived_bipartite_duplication	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	2081308	SO:0000547	SO:0001524	inversion_derived_bipartite_duplication	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	2081309	SO:0000549	SO:0001507	inversion_derived_duplication_plus_aneuploid	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	2081310	SO:0000549	SO:0001524	inversion_derived_duplication_plus_aneuploid	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]	SO	2081311	SO:0000550	SO:0001026	aneuploid_chromosome	SO:0001260
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081312	SO:0000551	SO:0000001	polyA_signal_sequence	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	2548785	SO:0000552	SO:0000673	Shine_Dalgarno_sequence	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	2961210	SO:0000552	SO:0001411	Shine_Dalgarno_sequence	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	SOFA	transcript	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081316	SO:0000553	SO:0000833	polyA_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081317	SO:0000553	SO:0000833	polyA_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2917077	SO:0000553	SO:0000001	polyA_site	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081319	SO:0000555	SO:0000831	five_prime_clip	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2548788	SO:0000555	SO:0000001	five_prime_clip	SO:0000110
6	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081321	SO:0000556	SO:0000299	five_prime_D_recombination_signal_sequence	SO:0000669
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2081322	SO:0000557	SO:0000831	three_prime_clip	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2548789	SO:0000557	SO:0000001	three_prime_clip	SO:0000110
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081324	SO:0000558	SO:0000669	C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081325	SO:0000559	SO:0000669	D_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081326	SO:0000560	SO:0000669	D_J_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081327	SO:0000561	SO:0000669	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"" []	SO	2081328	SO:0000562	SO:0000669	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000298
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2081329	SO:0000563	SO:0000298	vertebrate_immune_system_gene_recombination_spacer	SO:0001411
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081330	SO:0000564	SO:0000669	V_DJ_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081331	SO:0000565	SO:0000669	V_VDJ_J_C_cluster	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081332	SO:0000566	SO:0000669	V_VJ_J_C_cluster	SO:0000298
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	2081333	SO:0000567	SO:0001506	inversion_derived_aneuploid_chromosome	SO:0001026
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081334	SO:0000568	SO:0000831	bidirectional_promoter	SO:0001411
6	"" []	\N	sequence_rearrangement_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081335	SO:0000570	SO:0000299	three_prime_D_recombination_signal_sequence	SO:0000669
6	"" []	\N	recombination_feature	\N	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081336	SO:0000572	SO:0000669	DJ_gene_segment	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081337	SO:0000574	SO:0000669	VDJ_gene_segment	SO:0000298
6	"" []	\N	recombination_feature	\N	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2081338	SO:0000576	SO:0000669	VJ_gene_segment	SO:0000298
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	2081340	SO:0000580	SO:0000831	methylation_guide_snoRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	2081341	SO:0000582	SO:0000831	rRNA_cleavage_snoRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	2081343	SO:0000584	SO:0000831	tmRNA	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	SO	2081344	SO:0000586	SO:0001411	tmRNA_primary_transcript	SO:0000001
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	2081345	SO:0000587	SO:0000673	group_I_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	2706669	SO:0000587	SO:0001411	group_I_intron	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	2081347	SO:0000588	SO:0000831	autocatalytically_spliced_intron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A self spliced intron." [SO:ke]	SO	2548790	SO:0000588	SO:0000001	autocatalytically_spliced_intron	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	SO	2081349	SO:0000589	SO:0001411	SRP_RNA_primary_transcript	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SO	2081350	SO:0000590	SO:0001411	SRP_RNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	2081351	SO:0000593	SO:0000831	C_D_box_snoRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	2081352	SO:0000594	SO:0000831	H_ACA_box_snoRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	2081353	SO:0000595	SO:0000831	C_D_box_snoRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	2081354	SO:0000596	SO:0000831	H_ACA_box_snoRNA_primary_transcript	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SO	2081355	SO:0000602	SO:0001411	guide_RNA	SO:0000001
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	2081356	SO:0000603	SO:0000673	group_II_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	2706674	SO:0000603	SO:0001411	group_II_intron	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	2548791	SO:0000611	SO:0000831	branch_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]	SO	2917078	SO:0000611	SO:0000001	branch_site	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	2548793	SO:0000612	SO:0000831	polypyrimidine_tract	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]	SO	2917079	SO:0000612	SO:0000001	polypyrimidine_tract	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	2548795	SO:0000613	SO:0001411	bacterial_RNApol_promoter	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A terminator signal for bacterial transcription." [SO:ke]	SO	2279395	SO:0000614	SO:0000001	bacterial_terminator	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	2279396	SO:0000615	SO:0001411	terminator_of_type_2_RNApol_III_promoter	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	2081370	SO:0000617	SO:0001679	RNApol_III_promoter_type_1	SO:0005836
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	2081371	SO:0000618	SO:0001679	RNApol_III_promoter_type_2	SO:0005836
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	2081372	SO:0000619	SO:0001683	A_box	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	2081373	SO:0000620	SO:0001683	B_box	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	2081374	SO:0000620	SO:0001055	B_box	SO:0001679
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"" []	SO	2081375	SO:0000621	SO:0001679	RNApol_III_promoter_type_3	SO:0005836
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	2081376	SO:0000622	SO:0001683	C_box	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	2081377	SO:0000622	SO:0001055	C_box	SO:0001679
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	2081379	SO:0000625	SO:0000831	silencer	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SO	2081380	SO:0000627	SO:0001411	insulator	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2548796	SO:0000629	SO:0000831	five_prime_open_reading_frame	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2917080	SO:0000629	SO:0000001	five_prime_open_reading_frame	SO:0000110
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	2081383	SO:0000630	SO:0000673	upstream_AUG_codon	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	2706684	SO:0000630	SO:0001411	upstream_AUG_codon	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding for more than one gene product." [SO:ke]	SO	2081385	SO:0000631	SO:0000001	polycistronic_primary_transcript	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding for one gene product." [SO:ke]	SO	2081386	SO:0000632	SO:0000001	monocistronic_primary_transcript	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]	SO	2279397	SO:0000633	SO:0000001	monocistronic_mRNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]	SO	2279398	SO:0000634	SO:0000001	polycistronic_mRNA	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript that donates the spliced leader to other mRNA." [SO:ke]	SO	2081389	SO:0000635	SO:0000001	mini_exon_donor_RNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	2279399	SO:0000638	SO:0000831	transcribed_spacer_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]	SO	2764355	SO:0000638	SO:0000001	transcribed_spacer_region	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	2279400	SO:0000639	SO:0000673	internal_transcribed_spacer_region	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	2848890	SO:0000639	SO:0001411	internal_transcribed_spacer_region	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	2279401	SO:0000640	SO:0000673	external_transcribed_spacer_region	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	2848891	SO:0000640	SO:0001411	external_transcribed_spacer_region	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2081399	SO:0000641	SO:0001411	tetranucleotide_repeat_microsatellite_feature	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]	SO	2081400	SO:0000643	SO:0000001	minisatellite	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SO	2081401	SO:0000644	SO:0001411	antisense_RNA	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The reverse complement of the primary transcript." [SO:ke]	SO	2081402	SO:0000645	SO:0000001	antisense_primary_transcript	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SO	2081403	SO:0000646	SO:0001411	siRNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a micro RNA." [SO:ke]	SO	2081404	SO:0000647	SO:0001411	miRNA_primary_transcript	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	2081405	SO:0000648	SO:0000831	stRNA_primary_transcript	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SO	2081406	SO:0000649	SO:0001411	stRNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	2081407	SO:0000650	SO:0000831	small_subunit_rRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	2081408	SO:0000651	SO:0000831	large_subunit_rRNA	SO:0001411
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	2081409	SO:0000652	SO:0000673	rRNA_5S	SO:0000831
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	2081410	SO:0000653	SO:0000673	rRNA_28S	SO:0000831
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]	SO	2081411	SO:0000655	SO:0000001	ncRNA	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	2081412	SO:0000662	SO:0000831	spliceosomal_intron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An intron which is spliced by the spliceosome." [SO:ke]	SO	2548799	SO:0000662	SO:0000001	spliceosomal_intron	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]	SO	2081414	SO:0000666	SO:0000831	mobile_intron	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A match against an EST sequence." [SO:ke]	SO	2081415	SO:0000668	SO:0000001	EST_match	SO:0000110
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	2081416	SO:0000676	SO:0000185	canonical_three_prime_splice_site	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	2081417	SO:0000676	SO:0000833	canonical_three_prime_splice_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	2081418	SO:0000676	SO:0000833	canonical_three_prime_splice_site	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	2081419	SO:0000677	SO:0000185	canonical_five_prime_splice_site	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	2081420	SO:0000677	SO:0000833	canonical_five_prime_splice_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	2081421	SO:0000677	SO:0000833	canonical_five_prime_splice_site	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	2081422	SO:0000678	SO:0000185	non_canonical_three_prime_splice_site	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	2081423	SO:0000678	SO:0000833	non_canonical_three_prime_splice_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	2081424	SO:0000678	SO:0000833	non_canonical_three_prime_splice_site	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	2081425	SO:0000679	SO:0000185	non_canonical_five_prime_splice_site	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	2081426	SO:0000679	SO:0000833	non_canonical_five_prime_splice_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	2081427	SO:0000679	SO:0000833	non_canonical_five_prime_splice_site	SO:0001411
7	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2279402	SO:0000680	SO:0000234	non_canonical_start_codon	SO:0000233
7	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2279403	SO:0000680	SO:0000834	non_canonical_start_codon	SO:0000833
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	2081432	SO:0000683	SO:0000831	exonic_splice_enhancer	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SO	2081433	SO:0000684	SO:0001411	nuclease_sensitive_site	SO:0000001
6	"A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]	\N	binding_site	biosapiens,SOFA	SOFA	sequence	"" []	SO	2081434	SO:0000685	SO:0000410	DNAseI_hypersensitive_site	SO:0000409
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	2081435	SO:0000686	SO:0001507	translocation_element	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	2081436	SO:0000686	SO:0001524	translocation_element	SO:0001506
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A match against cDNA sequence." [SO:ke]	SO	2081437	SO:0000689	SO:0000001	cDNA_match	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes a transcript with stop codon readthrough." [SO:xp]	SO	2081438	SO:0000697	SO:0000001	gene_with_stop_codon_read_through	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]	SO	2279404	SO:0000698	SO:0000001	gene_with_stop_codon_redefined_as_pyrrolysine	SO:0000110
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	2081440	SO:0000706	SO:0000673	trans_splice_acceptor_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	2706705	SO:0000706	SO:0001411	trans_splice_acceptor_site	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	2081442	SO:0000707	SO:0000673	trans_splice_donor_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	2706706	SO:0000707	SO:0001411	trans_splice_donor_site	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	2081444	SO:0000708	SO:0000185	SL1_acceptor_site	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	2081445	SO:0000708	SO:0000833	SL1_acceptor_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	2081446	SO:0000708	SO:0000833	SL1_acceptor_site	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2081447	SO:0000709	SO:0000185	SL2_acceptor_site	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2081448	SO:0000709	SO:0000833	SL2_acceptor_site	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2081449	SO:0000709	SO:0000833	SL2_acceptor_site	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	SO	2081450	SO:0000710	SO:0001411	gene_with_stop_codon_redefined_as_selenocysteine	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene encoding a transcript that has a translational frameshift." [SO:xp]	SO	2081451	SO:0000712	SO:0000001	gene_with_transcript_with_translational_frameshift	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA that has the quality dicistronic." [SO:ke]	SO	2548800	SO:0000716	SO:0000001	dicistronic_mRNA	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]	SO	2081453	SO:0000719	SO:0000001	ultracontig	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes a dicistronic primary transcript." [SO:xp]	SO	2081455	SO:0000721	SO:0000001	gene_with_dicistronic_primary_transcript	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that encodes a polycistronic mRNA." [SO:xp]	SO	2081456	SO:0000722	SO:0000001	gene_with_dicistronic_mRNA	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SO	2081457	SO:0000727	SO:0001411	CRM	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	2081458	SO:0000734	SO:0001411	exemplar_mRNA	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2081459	SO:0000752	SO:0000001	gene_group_regulatory_region	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	2081462	SO:0000766	SO:0000831	pyrrolysyl_tRNA	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	2081463	SO:0000769	SO:0000233	tmRNA_coding_piece	SO:0000673
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	2548801	SO:0000769	SO:0000831	tmRNA_coding_piece	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	SO	2917081	SO:0000769	SO:0000001	tmRNA_coding_piece	SO:0000110
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	2081466	SO:0000770	SO:0000233	tmRNA_acceptor_piece	SO:0000673
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	2548803	SO:0000770	SO:0000831	tmRNA_acceptor_piece	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]	SO	2917082	SO:0000770	SO:0000001	tmRNA_acceptor_piece	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A mini_gene that rescues." [SO:xp]	SO	2081474	SO:0000795	SO:0000001	rescue_mini_gene	SO:0000110
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]	SO	2081477	SO:0000800	SO:0001026	assortment_derived_duplication	SO:0001260
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]	SO	2081478	SO:0000801	SO:0001026	assortment_derived_deficiency_plus_duplication	SO:0001260
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]	SO	2081479	SO:0000802	SO:0001026	assortment_derived_deficiency	SO:0001260
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]	SO	2081480	SO:0000803	SO:0001026	assortment_derived_aneuploid	SO:0001260
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cDNA clone that has been validated." [SO:xp]	SO	2081481	SO:0000808	SO:0000001	validated_cDNA_clone	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cDNA clone that is invalid." [SO:xp]	SO	2081482	SO:0000809	SO:0000001	invalidated_cDNA_clone	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cDNA clone invalidated because it is chimeric." [SO:xp]	SO	2081483	SO:0000810	SO:0001409	chimeric_cDNA_clone	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cDNA clone invalidated by genomic contamination." [SO:xp]	SO	2081484	SO:0000811	SO:0001409	genomically_contaminated_cDNA_clone	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cDNA clone invalidated by polyA priming." [SO:xp]	SO	2081485	SO:0000812	SO:0001409	polyA_primed_cDNA_clone	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cDNA invalidated clone by partial processing." [SO:xp]	SO	2081486	SO:0000813	SO:0001409	partially_processed_cDNA_clone	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	2081488	SO:0000837	SO:0000831	UTR_region	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of UTR." [SO:ke]	SO	2548805	SO:0000837	SO:0000001	UTR_region	SO:0000110
6	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081493	SO:0000848	SO:0001039	LTR_component	SO:0001037
6	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081494	SO:0000849	SO:0000101	three_prime_LTR_component	SO:0001039
6	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2081496	SO:0000850	SO:0000101	five_prime_LTR_component	SO:0001039
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	2279408	SO:0000851	SO:0000831	CDS_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of a CDS." [SO:cb]	SO	2764356	SO:0000851	SO:0000001	CDS_region	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript that is capped." [SO:xp]	SO	2081500	SO:0000861	SO:0000001	capped_primary_transcript	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA that is capped." [SO:xp]	SO	2081501	SO:0000862	SO:0001411	capped_mRNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA that is polyadenylated." [SO:xp]	SO	2081502	SO:0000871	SO:0001411	polyadenylated_mRNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA that is trans-spliced." [SO:xp]	SO	2279410	SO:0000872	SO:0000001	trans_spliced_mRNA	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that has been edited by A to I substitution." [SO:ke]	SO	2081504	SO:0000874	SO:0000001	edited_transcript_by_A_to_I_substitution	SO:0000110
7	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2279411	SO:0000883	SO:0000234	stop_codon_read_through	SO:0000233
7	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2279412	SO:0000883	SO:0000834	stop_codon_read_through	SO:0000833
6	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2081509	SO:0000884	SO:0000316	stop_codon_redefined_as_pyrrolysine	SO:0000836
7	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2441418	SO:0000884	SO:0000836	stop_codon_redefined_as_pyrrolysine	SO:0000234
7	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2441419	SO:0000884	SO:0000836	stop_codon_redefined_as_pyrrolysine	SO:0000834
6	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2081512	SO:0000885	SO:0000316	stop_codon_redefined_as_selenocysteine	SO:0000836
7	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2441422	SO:0000885	SO:0000836	stop_codon_redefined_as_selenocysteine	SO:0000234
7	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2441423	SO:0000885	SO:0000836	stop_codon_redefined_as_selenocysteine	SO:0000834
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]	SO	2081515	SO:0000893	SO:0000733	silenced	SO:0000400
6	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	SO	2081516	SO:0000894	SO:0000401	silenced_by_DNA_modification	SO:0000733
6	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	2081517	SO:0000895	SO:0000119	silenced_by_DNA_methylation	SO:0000401
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081518	SO:0000912	SO:0000104	asx_turn	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441428	SO:0000912	SO:0001411	asx_turn	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA that is edited." [SO:xp]	SO	2279413	SO:0000929	SO:0000001	edited_mRNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	2279415	SO:0000931	SO:0000831	anchor_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]	SO	2764357	SO:0000931	SO:0000001	anchor_region	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2081525	SO:0000932	SO:0001411	pre_edited_mRNA	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	2081526	SO:0000935	SO:0000673	edited_CDS	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	2706727	SO:0000935	SO:0001411	edited_CDS	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2081528	SO:0000936	SO:0000298	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2081529	SO:0000938	SO:0000298	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2081530	SO:0000939	SO:0000298	vertebrate_immune_system_gene_recombination_signal_feature	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	2081531	SO:0000942	SO:0000298	attP_site	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]	SO	2548810	SO:0000942	SO:0000001	attP_site	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	2081534	SO:0000943	SO:0000298	attB_site	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	2081535	SO:0000944	SO:0000298	attL_site	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	2081536	SO:0000945	SO:0000298	attR_site	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	SO	2081537	SO:0000946	SO:0001411	integration_excision_site	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	SO	2081538	SO:0000947	SO:0001411	resolution_site	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	SO	2081539	SO:0000948	SO:0001411	inversion_site	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	2081540	SO:0000949	SO:0000298	dif_site	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]	SO	2081541	SO:0000950	SO:0000298	attC_site	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2279417	SO:0000951	SO:0000001	eukaryotic_terminator	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]	SO	2081544	SO:0000955	SO:0000001	double_stranded_DNA_chromosome	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]	SO	2081545	SO:0000956	SO:0000001	single_stranded_DNA_chromosome	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	SO	2081546	SO:0000957	SO:0001411	linear_double_stranded_DNA_chromosome	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	SO	2081547	SO:0000958	SO:0001411	circular_double_stranded_DNA_chromosome	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	SO	2081548	SO:0000959	SO:0001411	linear_single_stranded_DNA_chromosome	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	2081549	SO:0000960	SO:0001411	circular_single_stranded_DNA_chromosome	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]	SO	2081550	SO:0000962	SO:0000001	single_stranded_RNA_chromosome	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	SO	2081551	SO:0000963	SO:0001411	linear_single_stranded_RNA_chromosome	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	SO	2081552	SO:0000964	SO:0001411	linear_double_stranded_RNA_chromosome	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]	SO	2081553	SO:0000965	SO:0000001	double_stranded_RNA_chromosome	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	2081554	SO:0000966	SO:0001411	circular_single_stranded_RNA_chromosome	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	SO	2081555	SO:0000967	SO:0001411	circular_double_stranded_RNA_chromosome	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	2081556	SO:0000973	SO:0001037	insertion_sequence	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	2081557	SO:0000973	SO:0001037	insertion_sequence	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	2279418	SO:0000978	SO:0000831	template_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]	SO	2764358	SO:0000978	SO:0000001	template_region	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2279419	SO:0000981	SO:0001411	rho_dependent_bacterial_terminator	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2279420	SO:0000982	SO:0001411	rho_independent_bacterial_terminator	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	2081565	SO:0000989	SO:0001411	class_II_RNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	2081566	SO:0000990	SO:0001411	class_I_RNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2279421	SO:0000992	SO:0000001	BAC_cloned_genomic_insert	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2081568	SO:0000995	SO:0001411	consensus_mRNA	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	2081569	SO:0000998	SO:0000673	recursive_splice_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	2706736	SO:0000998	SO:0001411	recursive_splice_site	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]	SO	2081574	SO:0000999	SO:0001409	BAC_end	SO:0000001
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	2081575	SO:0001000	SO:0000673	rRNA_16S	SO:0000831
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	2081576	SO:0001001	SO:0000673	rRNA_23S	SO:0000831
6	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	2081577	SO:0001002	SO:0000673	rRNA_25S	SO:0000831
6	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	2081578	SO:0001003	SO:0001039	solo_LTR	SO:0001037
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]	SO	2081581	SO:0001008	SO:0000001	tetraloop	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	SO	2081582	SO:0001009	SO:0000001	DNA_constraint_sequence	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]	SO	2081583	SO:0001011	SO:0000001	PNA_oligo	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	2548814	SO:0001016	SO:0000831	internal_guide_sequence	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]	SO	2917085	SO:0001016	SO:0000001	internal_guide_sequence	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The point within a chromosome where an inversion begins or ends." [SO:cb]	SO	2081587	SO:0001022	SO:0000001	inversion_breakpoint	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	2279426	SO:0001034	SO:0000831	mirtron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]	SO	2764361	SO:0001034	SO:0000001	mirtron	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	SO	2081590	SO:0001035	SO:0001411	piRNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	2081591	SO:0001036	SO:0000831	arginyl_tRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	2081592	SO:0001043	SO:0000298	attCtn_site	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	2081593	SO:0001043	SO:0001037	attCtn_site	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	2081594	SO:0001043	SO:0001037	attCtn_site	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	2081595	SO:0001046	SO:0000298	IRLinv_site	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	2081596	SO:0001047	SO:0000298	IRRinv_site	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region located within an inversion site." [SO:ke]	SO	2081597	SO:0001048	SO:0001411	inversion_site_part	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A portion of a transposon, interrupted by the insertion of another element." [SO:ke]	SO	2081600	SO:0001054	SO:0001411	transposon_fragment	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	SO	2081601	SO:0001055	SO:0000001	transcriptional_cis_regulatory_region	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A regulatory_region that modulates splicing." [SO:ke]	SO	2081602	SO:0001056	SO:0000001	splicing_regulatory_region	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	SO	2081603	SO:0001058	SO:0001411	promoter_targeting_sequence	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]	SO	2548817	SO:0001073	SO:0000001	cytoplasmic_polypeptide_region	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]	SO	2548818	SO:0001074	SO:0000001	non_cytoplasmic_polypeptide_region	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]	SO	2548819	SO:0001076	SO:0000001	membrane_peptide_loop	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]	SO	2548820	SO:0001077	SO:0000001	transmembrane_polypeptide_region	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]	SO	2279436	SO:0001080	SO:0000001	coiled_coil	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif comprising two helices separated by a turn." [EBIBS:GAR]	SO	2279437	SO:0001081	SO:0000001	helix_turn_helix	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	2081612	SO:0001089	SO:0000104	post_translationally_modified_region	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	2441479	SO:0001089	SO:0001411	post_translationally_modified_region	SO:0000001
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	2081614	SO:0001092	SO:0000839	polypeptide_metal_contact	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	2081615	SO:0001092	SO:0000839	polypeptide_metal_contact	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	2081616	SO:0001093	SO:0000839	protein_protein_contact	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	2081617	SO:0001093	SO:0000839	protein_protein_contact	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	2917086	SO:0001094	SO:0000001	polypeptide_calcium_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	2081619	SO:0001094	SO:0100021	polypeptide_calcium_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	2917087	SO:0001095	SO:0000001	polypeptide_cobalt_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	2081621	SO:0001095	SO:0100021	polypeptide_cobalt_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	2917088	SO:0001096	SO:0000001	polypeptide_copper_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	2081623	SO:0001096	SO:0100021	polypeptide_copper_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	2917089	SO:0001097	SO:0000001	polypeptide_iron_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	2081625	SO:0001097	SO:0100021	polypeptide_iron_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	2917090	SO:0001098	SO:0000001	polypeptide_magnesium_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	2081627	SO:0001098	SO:0100021	polypeptide_magnesium_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	2917091	SO:0001099	SO:0000001	polypeptide_manganese_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	2081629	SO:0001099	SO:0100021	polypeptide_manganese_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	2917092	SO:0001100	SO:0000001	polypeptide_molybdenum_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	2081631	SO:0001100	SO:0100021	polypeptide_molybdenum_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	2917093	SO:0001101	SO:0000001	polypeptide_nickel_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	2081633	SO:0001101	SO:0100021	polypeptide_nickel_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	2917094	SO:0001102	SO:0000001	polypeptide_tungsten_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	2081635	SO:0001102	SO:0100021	polypeptide_tungsten_ion_contact_site	SO:0000839
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	2917095	SO:0001103	SO:0000001	polypeptide_zinc_ion_contact_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	2081637	SO:0001103	SO:0100021	polypeptide_zinc_ion_contact_site	SO:0000839
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	2081638	SO:0001104	SO:0000839	catalytic_residue	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]	SO	2081639	SO:0001104	SO:0000839	catalytic_residue	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	2081640	SO:0001105	SO:0000839	polypeptide_ligand_contact	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	2081641	SO:0001105	SO:0000839	polypeptide_ligand_contact	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279438	SO:0001106	SO:0000001	asx_motif	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279439	SO:0001107	SO:0000001	beta_bulge	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279440	SO:0001108	SO:0000001	beta_bulge_loop	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081648	SO:0001109	SO:0000104	beta_bulge_loop_five	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441509	SO:0001109	SO:0001411	beta_bulge_loop_five	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081650	SO:0001110	SO:0000104	beta_bulge_loop_six	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441511	SO:0001110	SO:0001411	beta_bulge_loop_six	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]	SO	2279441	SO:0001111	SO:0000001	beta_strand	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	2081654	SO:0001112	SO:0000104	antiparallel_beta_strand	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	2441513	SO:0001112	SO:0001411	antiparallel_beta_strand	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	2081656	SO:0001113	SO:0000104	parallel_beta_strand	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	2441515	SO:0001113	SO:0001411	parallel_beta_strand	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]	SO	2279442	SO:0001114	SO:0000001	peptide_helix	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	2081660	SO:0001115	SO:0000104	left_handed_peptide_helix	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	2441517	SO:0001115	SO:0001411	left_handed_peptide_helix	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	2081662	SO:0001116	SO:0000104	right_handed_peptide_helix	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	2441519	SO:0001116	SO:0001411	right_handed_peptide_helix	SO:0000001
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	2081664	SO:0001117	SO:0000839	alpha_helix	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	2081665	SO:0001117	SO:0000839	alpha_helix	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	2081666	SO:0001118	SO:0000839	pi_helix	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	2081667	SO:0001118	SO:0000839	pi_helix	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	2081668	SO:0001119	SO:0000839	three_ten_helix	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	2081669	SO:0001119	SO:0000839	three_ten_helix	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279443	SO:0001120	SO:0000001	polypeptide_nest_motif	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081672	SO:0001121	SO:0000104	polypeptide_nest_left_right_motif	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441527	SO:0001121	SO:0001411	polypeptide_nest_left_right_motif	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081674	SO:0001122	SO:0000104	polypeptide_nest_right_left_motif	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441529	SO:0001122	SO:0001411	polypeptide_nest_right_left_motif	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279444	SO:0001123	SO:0000001	schellmann_loop	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081678	SO:0001124	SO:0000104	schellmann_loop_seven	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441531	SO:0001124	SO:0001411	schellmann_loop_seven	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081680	SO:0001125	SO:0000104	schellmann_loop_six	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441533	SO:0001125	SO:0001411	schellmann_loop_six	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279445	SO:0001126	SO:0000001	serine_threonine_motif	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279446	SO:0001127	SO:0000001	serine_threonine_staple_motif	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]	SO	2279447	SO:0001128	SO:0000001	polypeptide_turn_motif	SO:0000110
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081688	SO:0001129	SO:0000839	asx_turn_left_handed_type_one	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081689	SO:0001129	SO:0000839	asx_turn_left_handed_type_one	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081690	SO:0001130	SO:0000839	asx_turn_left_handed_type_two	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081691	SO:0001130	SO:0000839	asx_turn_left_handed_type_two	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081692	SO:0001131	SO:0000839	asx_turn_right_handed_type_two	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081693	SO:0001131	SO:0000839	asx_turn_right_handed_type_two	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081694	SO:0001132	SO:0000839	asx_turn_right_handed_type_one	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081695	SO:0001132	SO:0000839	asx_turn_right_handed_type_one	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081696	SO:0001133	SO:0000104	beta_turn	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441543	SO:0001133	SO:0001411	beta_turn	SO:0000001
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081698	SO:0001134	SO:0000839	beta_turn_left_handed_type_one	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081699	SO:0001134	SO:0000839	beta_turn_left_handed_type_one	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081700	SO:0001135	SO:0000839	beta_turn_left_handed_type_two	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081701	SO:0001135	SO:0000839	beta_turn_left_handed_type_two	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081702	SO:0001136	SO:0000839	beta_turn_right_handed_type_one	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081703	SO:0001136	SO:0000839	beta_turn_right_handed_type_one	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081704	SO:0001137	SO:0000839	beta_turn_right_handed_type_two	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081705	SO:0001137	SO:0000839	beta_turn_right_handed_type_two	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081706	SO:0001138	SO:0000104	gamma_turn	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441553	SO:0001138	SO:0001411	gamma_turn	SO:0000001
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081708	SO:0001139	SO:0000839	gamma_turn_classic	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081709	SO:0001139	SO:0000839	gamma_turn_classic	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081710	SO:0001140	SO:0000839	gamma_turn_inverse	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081711	SO:0001140	SO:0000839	gamma_turn_inverse	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081712	SO:0001141	SO:0000104	serine_threonine_turn	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441559	SO:0001141	SO:0001411	serine_threonine_turn	SO:0000001
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081714	SO:0001142	SO:0000839	st_turn_left_handed_type_one	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081715	SO:0001142	SO:0000839	st_turn_left_handed_type_one	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081716	SO:0001143	SO:0000839	st_turn_left_handed_type_two	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081717	SO:0001143	SO:0000839	st_turn_left_handed_type_two	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081718	SO:0001144	SO:0000839	st_turn_right_handed_type_one	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081719	SO:0001144	SO:0000839	st_turn_right_handed_type_one	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081720	SO:0001145	SO:0000839	st_turn_right_handed_type_two	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2081721	SO:0001145	SO:0000839	st_turn_right_handed_type_two	SO:0001411
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	2081722	SO:0001150	SO:0000839	beta_turn_type_six	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	2081723	SO:0001150	SO:0000839	beta_turn_type_six	SO:0001411
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2081724	SO:0001151	SO:0001070	beta_turn_type_six_a	SO:0000839
6	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"" []	SO	2081725	SO:0001152	SO:0001078	beta_turn_type_six_a_one	SO:0001070
6	"Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]	biosapiens	polypeptide_structural_region	biosapiens	biosapiens	sequence	"" []	SO	2081726	SO:0001153	SO:0001078	beta_turn_type_six_a_two	SO:0001070
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2081727	SO:0001154	SO:0001070	beta_turn_type_six_b	SO:0000839
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	2081728	SO:0001155	SO:0000839	beta_turn_type_eight	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	2081729	SO:0001155	SO:0000839	beta_turn_type_eight	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	2917096	SO:0001156	SO:0000001	DRE_motif	SO:0000110
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	2081731	SO:0001156	SO:0001679	DRE_motif	SO:0005836
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	SO	2081732	SO:0001157	SO:0001411	DMv4_motif	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	2917097	SO:0001158	SO:0000001	E_box_motif	SO:0000110
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	2081734	SO:0001158	SO:0001679	E_box_motif	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2885758	SO:0001159	SO:0001411	DMv5_motif	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2081736	SO:0001159	SO:0001679	DMv5_motif	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	2885759	SO:0001160	SO:0001411	DMv3_motif	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	2081738	SO:0001160	SO:0001679	DMv3_motif	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2885760	SO:0001161	SO:0001411	DMv2_motif	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2081740	SO:0001161	SO:0001679	DMv2_motif	SO:0005836
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	2081741	SO:0001162	SO:0001683	MTE	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	2081742	SO:0001162	SO:0001055	MTE	SO:0001679
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	2917098	SO:0001163	SO:0000001	INR1_motif	SO:0000110
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	2081744	SO:0001163	SO:0001679	INR1_motif	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	2885763	SO:0001164	SO:0001411	DPE1_motif	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	2081746	SO:0001164	SO:0001679	DPE1_motif	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	2885764	SO:0001165	SO:0001411	DMv1_motif	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	2081748	SO:0001165	SO:0001679	DMv1_motif	SO:0005836
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	2917099	SO:0001166	SO:0000001	GAGA_motif	SO:0000110
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	2081750	SO:0001166	SO:0001679	GAGA_motif	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	2885766	SO:0001167	SO:0001411	NDM2_motif	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	2081752	SO:0001167	SO:0001679	NDM2_motif	SO:0005836
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	2885767	SO:0001168	SO:0001411	NDM3_motif	SO:0000001
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	2081754	SO:0001168	SO:0001679	NDM3_motif	SO:0005836
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	2081755	SO:0001170	SO:0001037	polinton	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	2081756	SO:0001170	SO:0001037	polinton	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	2081757	SO:0001171	SO:0000673	rRNA_21S	SO:0000831
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	2279449	SO:0001173	SO:0000831	anticodon_loop	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]	SO	2764372	SO:0001173	SO:0000001	anticodon_loop	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	2548822	SO:0001174	SO:0000831	anticodon	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]	SO	2917100	SO:0001174	SO:0000001	anticodon	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	2279453	SO:0001175	SO:0000831	CCA_tail	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]	SO	2764374	SO:0001175	SO:0000001	CCA_tail	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	2279454	SO:0001176	SO:0000831	DHU_loop	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]	SO	2764375	SO:0001176	SO:0000001	DHU_loop	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	2279455	SO:0001177	SO:0000831	T_loop	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]	SO	2764376	SO:0001177	SO:0000001	T_loop	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	2081773	SO:0001178	SO:0000831	pyrrolysine_tRNA_primary_transcript	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	2081774	SO:0001179	SO:0000673	U3_snoRNA	SO:0000831
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	2279456	SO:0001180	SO:0000673	AU_rich_element	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	2848921	SO:0001180	SO:0001411	AU_rich_element	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	2279458	SO:0001181	SO:0000673	Bruno_response_element	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	2848922	SO:0001181	SO:0001411	Bruno_response_element	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	2081779	SO:0001182	SO:0000673	iron_responsive_element	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	2706834	SO:0001182	SO:0001411	iron_responsive_element	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	2081781	SO:0001187	SO:0000673	pseudouridylation_guide_snoRNA	SO:0000831
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An oligo composed of LNA residues." [RSC:cb]	SO	2081782	SO:0001189	SO:0000001	LNA_oligo	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An oligo composed of TNA residues." [RSC:cb]	SO	2081783	SO:0001191	SO:0000001	TNA_oligo	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An oligo composed of GNA residues." [RSC:cb]	SO	2081784	SO:0001193	SO:0000001	GNA_oligo	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An oligo composed of (R)-GNA residues." [RSC:cb]	SO	2081785	SO:0001195	SO:0001409	R_GNA_oligo	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An oligo composed of (S)-GNA residues." [RSC:cb]	SO	2081786	SO:0001197	SO:0001409	S_GNA_oligo	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]	SO	2279460	SO:0001200	SO:0000001	negative_sense_ssRNA_viral_sequence	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]	SO	2279461	SO:0001201	SO:0000001	positive_sense_ssRNA_viral_sequence	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]	SO	2279462	SO:0001202	SO:0000001	ambisense_ssRNA_viral_sequence	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2081793	SO:0001203	SO:0000831	RNA_polymerase_promoter	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2081794	SO:0001204	SO:0005836	Phage_RNA_Polymerase_Promoter	SO:0000831
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2081795	SO:0001205	SO:0001679	SP6_RNA_Polymerase_Promoter	SO:0005836
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2081796	SO:0001206	SO:0001679	T3_RNA_Polymerase_Promoter	SO:0005836
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2081797	SO:0001207	SO:0001679	T7_RNA_Polymerase_Promoter	SO:0005836
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	2081798	SO:0001208	SO:0001409	five_prime_EST	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	2081799	SO:0001209	SO:0001409	three_prime_EST	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2081800	SO:0001210	SO:0000831	translational_frameshift	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2548827	SO:0001210	SO:0000001	translational_frameshift	SO:0000110
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2081802	SO:0001211	SO:0000673	plus_1_translational_frameshift	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2706841	SO:0001211	SO:0001411	plus_1_translational_frameshift	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2081804	SO:0001212	SO:0000673	plus_2_translational_frameshift	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2706842	SO:0001212	SO:0001411	plus_2_translational_frameshift	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	2081806	SO:0001213	SO:0000673	group_III_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	2706843	SO:0001213	SO:0001411	group_III_intron	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	2081810	SO:0001216	SO:0000831	endonuclease_spliced_intron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	2548828	SO:0001216	SO:0000001	endonuclease_spliced_intron	SO:0000110
6	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	SO	2081812	SO:0001220	SO:0000401	silenced_by_RNA_interference	SO:0000733
6	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	SO	2081813	SO:0001221	SO:0000401	silenced_by_histone_modification	SO:0000733
6	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	2081814	SO:0001222	SO:0000119	silenced_by_histone_methylation	SO:0000401
6	"" []	\N	gene_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	2081815	SO:0001223	SO:0000119	silenced_by_histone_deacetylation	SO:0000401
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is silenced by histone methylation." [SO:xp]	SO	2081816	SO:0001226	SO:0000001	gene_silenced_by_histone_methylation	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene that is silenced by histone deacetylation." [SO:xp]	SO	2081817	SO:0001227	SO:0000001	gene_silenced_by_histone_deacetylation	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]	SO	2081818	SO:0001228	SO:0000001	dihydrouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]	SO	2081819	SO:0001229	SO:0000001	pseudouridine	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	SO	2081820	SO:0001233	SO:0001411	methylinosine	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081821	SO:0001238	SO:0000831	major_TSS	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2548829	SO:0001238	SO:0000001	major_TSS	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2081823	SO:0001239	SO:0000831	minor_TSS	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2548830	SO:0001239	SO:0000001	minor_TSS	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	2081826	SO:0001244	SO:0000831	pre_miRNA	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]	SO	2548831	SO:0001244	SO:0000001	pre_miRNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	2279465	SO:0001245	SO:0000831	miRNA_stem	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	2764377	SO:0001245	SO:0000001	miRNA_stem	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	2279467	SO:0001246	SO:0000831	miRNA_loop	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]	SO	2764378	SO:0001246	SO:0000001	miRNA_loop	SO:0000110
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]	SO	2081832	SO:0001254	SO:0001026	polyploid	SO:0001260
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	2081833	SO:0001255	SO:0001506	autopolyploid	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	2081834	SO:0001256	SO:0001506	allopolyploid	SO:0001026
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	SO	2081835	SO:0001257	SO:0001411	homing_endonuclease_binding_site	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	2917101	SO:0001258	SO:0000001	octamer_motif	SO:0000110
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	2081837	SO:0001258	SO:0001679	octamer_motif	SO:0005836
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]	SO	2081838	SO:0001262	SO:0000001	overlapping_EST_set	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified inosine is an inosine base feature that has been altered." [SO:ke]	SO	2081839	SO:0001274	SO:0000001	modified_inosine	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	2081840	SO:0001278	SO:0001411	one_methylinosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	2081841	SO:0001279	SO:0001411	one_two_prime_O_dimethylinosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	2081842	SO:0001280	SO:0001411	two_prime_O_methylinosine	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081843	SO:0001281	SO:0000001	three_methylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081844	SO:0001282	SO:0000001	five_methylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081845	SO:0001283	SO:0000001	two_prime_O_methylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081846	SO:0001284	SO:0000001	two_thiocytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081847	SO:0001285	SO:0000001	N4_acetylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081848	SO:0001286	SO:0000001	five_formylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081849	SO:0001287	SO:0000001	five_two_prime_O_dimethylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081850	SO:0001288	SO:0000001	N4_acetyl_2_prime_O_methylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081851	SO:0001289	SO:0000001	lysidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081852	SO:0001290	SO:0000001	N4_methylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081853	SO:0001291	SO:0000001	N4_2_prime_O_dimethylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081854	SO:0001292	SO:0000001	five_hydroxymethylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081855	SO:0001293	SO:0000001	five_formyl_two_prime_O_methylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]	SO	2081856	SO:0001294	SO:0000001	N4_N4_2_prime_O_trimethylcytidine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081857	SO:0001295	SO:0000001	one_methyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081858	SO:0001296	SO:0000001	two_methyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081859	SO:0001297	SO:0000001	N6_methyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081860	SO:0001298	SO:0000001	two_prime_O_methyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081861	SO:0001299	SO:0000001	two_methylthio_N6_methyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081862	SO:0001300	SO:0000001	N6_isopentenyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081863	SO:0001301	SO:0000001	two_methylthio_N6_isopentenyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081864	SO:0001302	SO:0000001	N6_cis_hydroxyisopentenyl_adenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081865	SO:0001303	SO:0000001	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081866	SO:0001304	SO:0000001	N6_glycinylcarbamoyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081867	SO:0001305	SO:0000001	N6_threonylcarbamoyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081868	SO:0001306	SO:0000001	two_methylthio_N6_threonyl_carbamoyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081869	SO:0001307	SO:0000001	N6_methyl_N6_threonylcarbamoyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081870	SO:0001308	SO:0000001	N6_hydroxynorvalylcarbamoyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081871	SO:0001309	SO:0000001	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081872	SO:0001310	SO:0000001	two_prime_O_ribosyladenosine_phosphate	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081873	SO:0001311	SO:0000001	N6_N6_dimethyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081874	SO:0001312	SO:0000001	N6_2_prime_O_dimethyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081875	SO:0001313	SO:0000001	N6_N6_2_prime_O_trimethyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081876	SO:0001314	SO:0000001	one_two_prime_O_dimethyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]	SO	2081877	SO:0001315	SO:0000001	N6_acetyladenosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]	SO	2081878	SO:0001316	SO:0000001	seven_deazaguanosine	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2081879	SO:0001317	SO:0001411	queuosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2081880	SO:0001318	SO:0001411	epoxyqueuosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2081881	SO:0001319	SO:0001411	galactosyl_queuosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2081882	SO:0001320	SO:0001411	mannosyl_queuosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2081883	SO:0001321	SO:0001411	seven_cyano_seven_deazaguanosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2081884	SO:0001322	SO:0001411	seven_aminomethyl_seven_deazaguanosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2081885	SO:0001323	SO:0001411	archaeosine	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081886	SO:0001324	SO:0000001	one_methylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081887	SO:0001325	SO:0000001	N2_methylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081888	SO:0001326	SO:0000001	seven_methylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081889	SO:0001327	SO:0000001	two_prime_O_methylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081890	SO:0001328	SO:0000001	N2_N2_dimethylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081891	SO:0001329	SO:0000001	N2_2_prime_O_dimethylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081892	SO:0001330	SO:0000001	N2_N2_2_prime_O_trimethylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081893	SO:0001331	SO:0000001	two_prime_O_ribosylguanosine_phosphate	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081894	SO:0001332	SO:0000001	wybutosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081895	SO:0001333	SO:0000001	peroxywybutosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081896	SO:0001334	SO:0000001	hydroxywybutosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081897	SO:0001335	SO:0000001	undermodified_hydroxywybutosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081898	SO:0001336	SO:0000001	wyosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081899	SO:0001337	SO:0000001	methylwyosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081900	SO:0001338	SO:0000001	N2_7_dimethylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081901	SO:0001339	SO:0000001	N2_N2_7_trimethylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081902	SO:0001340	SO:0000001	one_two_prime_O_dimethylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081903	SO:0001341	SO:0000001	four_demethylwyosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081904	SO:0001342	SO:0000001	isowyosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081905	SO:0001343	SO:0000001	N2_7_2prirme_O_trimethylguanosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081906	SO:0001344	SO:0000001	five_methyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081907	SO:0001345	SO:0000001	two_prime_O_methyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081908	SO:0001346	SO:0000001	five_two_prime_O_dimethyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081909	SO:0001347	SO:0000001	one_methylpseudouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081910	SO:0001348	SO:0000001	two_prime_O_methylpseudouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081911	SO:0001349	SO:0000001	two_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081912	SO:0001350	SO:0000001	four_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081913	SO:0001351	SO:0000001	five_methyl_2_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081914	SO:0001352	SO:0000001	two_thio_two_prime_O_methyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081915	SO:0001353	SO:0000001	three_three_amino_three_carboxypropyl_uridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081916	SO:0001354	SO:0000001	five_hydroxyuridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081917	SO:0001355	SO:0000001	five_methoxyuridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081918	SO:0001356	SO:0000001	uridine_five_oxyacetic_acid	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081919	SO:0001357	SO:0000001	uridine_five_oxyacetic_acid_methyl_ester	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081920	SO:0001358	SO:0000001	five_carboxyhydroxymethyl_uridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081921	SO:0001359	SO:0000001	five_carboxyhydroxymethyl_uridine_methyl_ester	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081922	SO:0001360	SO:0000001	five_methoxycarbonylmethyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081923	SO:0001361	SO:0000001	five_methoxycarbonylmethyl_two_prime_O_methyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081924	SO:0001362	SO:0000001	five_methoxycarbonylmethyl_two_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081925	SO:0001363	SO:0000001	five_aminomethyl_two_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081926	SO:0001364	SO:0000001	five_methylaminomethyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081927	SO:0001365	SO:0000001	five_methylaminomethyl_two_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081928	SO:0001366	SO:0000001	five_methylaminomethyl_two_selenouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081929	SO:0001367	SO:0000001	five_carbamoylmethyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081930	SO:0001368	SO:0000001	five_carbamoylmethyl_two_prime_O_methyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081931	SO:0001369	SO:0000001	five_carboxymethylaminomethyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081932	SO:0001370	SO:0000001	five_carboxymethylaminomethyl_two_prime_O_methyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081933	SO:0001371	SO:0000001	five_carboxymethylaminomethyl_two_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081934	SO:0001372	SO:0000001	three_methyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081935	SO:0001373	SO:0000001	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081936	SO:0001374	SO:0000001	five_carboxymethyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081937	SO:0001375	SO:0000001	three_two_prime_O_dimethyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081938	SO:0001376	SO:0000001	five_methyldihydrouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081939	SO:0001377	SO:0000001	three_methylpseudouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081940	SO:0001378	SO:0000001	five_taurinomethyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081941	SO:0001379	SO:0000001	five_taurinomethyl_two_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081942	SO:0001380	SO:0000001	five_isopentenylaminomethyl_uridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081943	SO:0001381	SO:0000001	five_isopentenylaminomethyl_two_thiouridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]	SO	2081944	SO:0001382	SO:0000001	five_isopentenylaminomethyl_two_prime_O_methyluridine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]	SO	2081945	SO:0001383	SO:0000001	histone_binding_site	SO:0000110
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2081946	SO:0001384	SO:0000673	CDS_fragment	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706847	SO:0001384	SO:0001411	CDS_fragment	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The point within a chromosome where a translocation begins or ends." [SO:cb]	SO	2081948	SO:0001413	SO:0000001	translocation_breakpoint	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The point within a chromosome where a insertion begins or ends." [SO:cb]	SO	2081949	SO:0001414	SO:0000001	insertion_breakpoint	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The point within a chromosome where a deletion begins or ends." [SO:cb]	SO	2081950	SO:0001415	SO:0000001	deletion_breakpoint	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	2081951	SO:0001419	SO:0000831	cis_splice_site	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]	SO	2548834	SO:0001419	SO:0000001	cis_splice_site	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	2081953	SO:0001420	SO:0000831	trans_splice_site	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Primary transcript region bordering trans-splice junction." [SO:ke]	SO	2548835	SO:0001420	SO:0000001	trans_splice_site	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	2081955	SO:0001422	SO:0000104	conformational_switch	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	2441662	SO:0001422	SO:0001411	conformational_switch	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]	SO	2081969	SO:0001427	SO:0000001	cis_regulatory_frameshift_element	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]	SO	2081970	SO:0001433	SO:0000001	three_prime_RACE_clone	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	2548840	SO:0001460	SO:0000001	insulator_binding_site	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	2081972	SO:0001460	SO:0000831	insulator_binding_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	2764383	SO:0001461	SO:0000001	enhancer_binding_site	SO:0000110
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	2081974	SO:0001461	SO:0005836	enhancer_binding_site	SO:0000831
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A collection of contigs." [SO:ke]	SO	2081975	SO:0001462	SO:0000001	contig_collection	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	2081976	SO:0001463	SO:0000831	lincRNA	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	SO	2081977	SO:0001464	SO:0001409	UST	SO:0000001
6	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	2081978	SO:0001465	SO:0000695	three_prime_UST	SO:0001409
6	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	2081979	SO:0001466	SO:0000695	five_prime_UST	SO:0001409
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	2081980	SO:0001467	SO:0001409	RST	SO:0000001
6	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	2081981	SO:0001468	SO:0000695	three_prime_RST	SO:0001409
6	"A region which is intended for use in an experiment." [SO:cb]	\N	biomaterial_region	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	2081982	SO:0001469	SO:0000695	five_prime_RST	SO:0001409
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A match against an UST sequence." [SO:nlw]	SO	2081983	SO:0001470	SO:0000001	UST_match	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A match against an RST sequence." [SO:nlw]	SO	2081984	SO:0001471	SO:0000001	RST_match	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	2081985	SO:0001473	SO:0000831	miRNA_antiguide	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]	SO	2548841	SO:0001473	SO:0000001	miRNA_antiguide	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]	SO	2081994	SO:0001480	SO:0001409	PAC_end	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2081995	SO:0001482	SO:0005836	shadow_enhancer	SO:0000831
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]	SO	2081996	SO:0001484	SO:0001235	X_element_combinatorial_repeat	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]	SO	2081997	SO:0001485	SO:0001235	Y_prime_element	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A regulatory region that is part of an intron." [SO:ke]	SO	2548843	SO:0001492	SO:0000001	intronic_regulatory_region	SO:0000110
6	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	2082000	SO:0001493	SO:0000340	centromere_DNA_Element_I	SO:0001235
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	2706855	SO:0001493	SO:0001411	centromere_DNA_Element_I	SO:0000001
6	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	2082002	SO:0001494	SO:0000340	centromere_DNA_Element_II	SO:0001235
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	2706856	SO:0001494	SO:0001411	centromere_DNA_Element_II	SO:0000001
6	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	2082004	SO:0001495	SO:0000340	centromere_DNA_Element_III	SO:0001235
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	2706857	SO:0001495	SO:0001411	centromere_DNA_Element_III	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]	SO	2082006	SO:0001496	SO:0001235	telomeric_repeat	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	SO	2082007	SO:0001497	SO:0001235	X_element	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]	SO	2082012	SO:0001498	SO:0001409	YAC_end	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region recognized by a recombinase." [SO:ke]	SO	2082013	SO:0001532	SO:0000001	recombination_signal_sequence	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	2082014	SO:0001533	SO:0000831	cryptic_splice_site	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]	SO	2548846	SO:0001533	SO:0000001	cryptic_splice_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	2441686	SO:0001535	SO:0000001	p_element	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]	SO	2082017	SO:0001535	SO:0001411	p_element	SO:0000001
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	2082018	SO:0001567	SO:0001564	stop_retained_variant	SO:0001878
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	2082019	SO:0001569	SO:0001537	cryptic_splice_site_variant	SO:0001060
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	SO	2082020	SO:0001570	SO:0001878	cryptic_splice_acceptor	SO:0001537
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	SO	2082021	SO:0001571	SO:0001878	cryptic_splice_donor	SO:0001537
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby an exon is lost from the transcript." [SO:ke]	SO	2082022	SO:0001572	SO:0001537	exon_loss_variant	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	2082023	SO:0001573	SO:0001537	intron_gain	SO:0001060
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	2082024	SO:0001574	SO:0001878	splice_acceptor_variant	SO:0001537
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	2082025	SO:0001575	SO:0001878	splice_donor_variant	SO:0001537
8	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]	SO	2548847	SO:0001578	SO:0001564	stop_lost	SO:0001878
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes the coding sequence." [SO:ke]	SO	2082027	SO:0001580	SO:0001537	coding_sequence_variant	SO:0001060
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	2082028	SO:0001582	SO:0001878	initiator_codon_variant	SO:0001537
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	2082029	SO:0001583	SO:0001791	missense_variant	SO:0001576
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	2082030	SO:0001583	SO:0001968	missense_variant	SO:0001576
6	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	2082031	SO:0001585	SO:0001580	conservative_missense_variant	SO:0001791
6	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	2082032	SO:0001585	SO:0001580	conservative_missense_variant	SO:0001968
6	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	2082033	SO:0001586	SO:0001580	non_conservative_missense_variant	SO:0001791
6	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	2082034	SO:0001586	SO:0001580	non_conservative_missense_variant	SO:0001968
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	2082035	SO:0001587	SO:0001791	stop_gained	SO:0001576
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	2082036	SO:0001587	SO:0001968	stop_gained	SO:0001576
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	2082037	SO:0001589	SO:0001564	frameshift_variant	SO:0001878
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	2082038	SO:0001590	SO:0001878	terminator_codon_variant	SO:0001537
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	2082039	SO:0001591	SO:0001576	frame_restoring_variant	SO:0001564
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	2082040	SO:0001592	SO:0001576	minus_1_frameshift_variant	SO:0001564
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"" []	SO	2082041	SO:0001593	SO:0001576	minus_2_frameshift_variant	SO:0001564
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	2082042	SO:0001594	SO:0001576	plus_1_frameshift_variant	SO:0001564
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"" []	SO	2082043	SO:0001595	SO:0001576	plus_2_frameshift_variant	SO:0001564
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]	SO	2082044	SO:0001597	SO:0001537	compensatory_transcript_secondary_structure_variant	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]	SO	2082045	SO:0001604	SO:0001537	amino_acid_deletion	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]	SO	2082046	SO:0001605	SO:0001537	amino_acid_insertion	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]	SO	2082047	SO:0001606	SO:0001537	amino_acid_substitution	SO:0001060
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	SO	2082048	SO:0001607	SO:0001878	conservative_amino_acid_substitution	SO:0001537
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	SO	2082049	SO:0001608	SO:0001878	non_conservative_amino_acid_substitution	SO:0001537
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]	SO	2082050	SO:0001609	SO:0001537	elongated_polypeptide	SO:0001060
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	2082051	SO:0001610	SO:0001878	elongated_polypeptide_C_terminal	SO:0001537
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	2082052	SO:0001611	SO:0001878	elongated_polypeptide_N_terminal	SO:0001537
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	2082053	SO:0001612	SO:0001564	elongated_in_frame_polypeptide_C_terminal	SO:0001878
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	2082054	SO:0001613	SO:0001564	elongated_out_of_frame_polypeptide_C_terminal	SO:0001878
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	2082055	SO:0001614	SO:0001564	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001878
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	2082056	SO:0001615	SO:0001564	elongated_out_of_frame_polypeptide_N_terminal	SO:0001878
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]	SO	2082057	SO:0001616	SO:0001537	polypeptide_fusion	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]	SO	2082058	SO:0001617	SO:0001537	polypeptide_truncation	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]	SO	2082059	SO:0001618	SO:0001536	inactive_catalytic_site	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant located with the sequence of the mature miRNA." [SO:ke]	SO	2082060	SO:0001620	SO:0001537	mature_miRNA_variant	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant that is located within the UTR." [SO:ke]	SO	2082061	SO:0001622	SO:0001537	UTR_variant	SO:0001060
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	2082062	SO:0001623	SO:0001878	5_prime_UTR_variant	SO:0001537
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	2082063	SO:0001624	SO:0001878	3_prime_UTR_variant	SO:0001537
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	2279475	SO:0001626	SO:0001564	incomplete_terminal_codon_variant	SO:0001878
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]	SO	2082065	SO:0001629	SO:0001537	splice_site_variant	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]	SO	2082066	SO:0001630	SO:0001537	splice_region_variant	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located within a half KB of the end of a gene." [SO:ke]	SO	2082067	SO:0001634	SO:0001537	500B_downstream_variant	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant located within 2KB 5' of a gene." [SO:ke]	SO	2082068	SO:0001636	SO:0001537	2KB_upstream_variant	SO:0001060
8	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	2548848	SO:0001647	SO:0000673	kozak_sequence	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	2961217	SO:0001647	SO:0001411	kozak_sequence	SO:0000001
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	2082072	SO:0001650	SO:0001564	inframe_variant	SO:0001878
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	2548850	SO:0001653	SO:0000001	retinoic_acid_responsive_element	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]	SO	2082074	SO:0001653	SO:0000831	retinoic_acid_responsive_element	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2082075	SO:0001659	SO:0000001	promoter_element	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2082076	SO:0001660	SO:0001411	core_promoter_element	SO:0000001
6	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	2082077	SO:0001661	SO:0000714	RNA_polymerase_II_TATA_box	SO:0001683
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	2082078	SO:0001661	SO:0001055	RNA_polymerase_II_TATA_box	SO:0001679
6	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	2082079	SO:0001662	SO:0000714	RNA_polymerase_III_TATA_box	SO:0001683
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	2082080	SO:0001662	SO:0001679	RNA_polymerase_III_TATA_box	SO:0005836
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	2082081	SO:0001663	SO:0001683	BREd_motif	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	2082082	SO:0001663	SO:0001055	BREd_motif	SO:0001679
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	2082083	SO:0001664	SO:0001683	DCE	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	2082084	SO:0001664	SO:0001055	DCE	SO:0001679
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	3064778	SO:0001665	SO:0000001	DCE_SI	SO:0000110
6	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	2082086	SO:0001665	SO:0000167	DCE_SI	SO:0001055
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	3064779	SO:0001666	SO:0000001	DCE_SII	SO:0000110
6	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	2082088	SO:0001666	SO:0000167	DCE_SII	SO:0001055
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	3064780	SO:0001667	SO:0000001	DCE_SIII	SO:0000110
6	"A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]	\N	transcriptional_cis_regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	2082090	SO:0001667	SO:0000167	DCE_SIII	SO:0001055
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	2082091	SO:0001668	SO:0001683	proximal_promoter_element	SO:0001411
6	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	2082092	SO:0001669	SO:0001679	RNApol_II_core_promoter	SO:0005836
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2082093	SO:0001670	SO:0001683	distal_promoter_element	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2548851	SO:0001671	SO:0000831	bacterial_RNApol_promoter_sigma_70	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2548852	SO:0001672	SO:0000831	bacterial_RNApol_promoter_sigma54	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	3011586	SO:0001673	SO:0000001	minus_12_signal	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2548853	SO:0001673	SO:0005836	minus_12_signal	SO:0000831
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2082100	SO:0001673	SO:0001055	minus_12_signal	SO:0001679
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	3011587	SO:0001674	SO:0000001	minus_24_signal	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2548854	SO:0001674	SO:0005836	minus_24_signal	SO:0000831
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2082103	SO:0001674	SO:0001055	minus_24_signal	SO:0001679
6	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	2082104	SO:0001675	SO:0000714	A_box_type_1	SO:0001683
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	2082105	SO:0001675	SO:0001055	A_box_type_1	SO:0001679
6	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	2082106	SO:0001676	SO:0000714	A_box_type_2	SO:0001683
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	2082107	SO:0001676	SO:0001055	A_box_type_2	SO:0001679
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	2082108	SO:0001677	SO:0001683	intermediate_element	SO:0001411
6	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	2082109	SO:0001677	SO:0001055	intermediate_element	SO:0001679
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	SO	2082110	SO:0001678	SO:0001411	regulatory_promoter_element	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]	SO	2082111	SO:0001689	SO:0000001	five_prime_restriction_enzyme_junction	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2082112	SO:0001690	SO:0000001	three_prime_restriction_enzyme_junction	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]	SO	2082113	SO:0001693	SO:0000001	blunt_end_restriction_enzyme_cleavage_junction	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	SO	2082114	SO:0001698	SO:0001409	ASPE_primer	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	SO	2082115	SO:0001699	SO:0001409	dCAPS_primer	SO:0000001
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	2082116	SO:0001700	SO:0000839	histone_modification	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	2082117	SO:0001700	SO:0000839	histone_modification	SO:0001411
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	2082118	SO:0001701	SO:0100021	histone_methylation_site	SO:0000839
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	2082119	SO:0001702	SO:0100021	histone_acetylation_site	SO:0000839
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082120	SO:0001703	SO:0100001	H3K9_acetylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056751	SO:0001703	SO:0001411	H3K9_acetylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082122	SO:0001704	SO:0100001	H3K14_acetylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056752	SO:0001704	SO:0001411	H3K14_acetylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082124	SO:0001705	SO:0100001	H3K4_monomethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056753	SO:0001705	SO:0001411	H3K4_monomethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082126	SO:0001706	SO:0100001	H3K4_trimethylation	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056754	SO:0001706	SO:0001411	H3K4_trimethylation	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082128	SO:0001707	SO:0100001	H3K9_trimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056755	SO:0001707	SO:0001411	H3K9_trimethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082130	SO:0001708	SO:0100001	H3K27_monomethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056756	SO:0001708	SO:0001411	H3K27_monomethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082132	SO:0001709	SO:0100001	H3K27_trimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056757	SO:0001709	SO:0001411	H3K27_trimethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082134	SO:0001710	SO:0100001	H3K79_monomethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056758	SO:0001710	SO:0001411	H3K79_monomethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082136	SO:0001711	SO:0100001	H3K79_dimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056759	SO:0001711	SO:0001411	H3K79_dimethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082138	SO:0001712	SO:0100001	H3K79_trimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3056760	SO:0001712	SO:0001411	H3K79_trimethylation_site	SO:0000001
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082140	SO:0001713	SO:0001067	H4K20_monomethylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3011588	SO:0001713	SO:0000001	H4K20_monomethylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2082142	SO:0001714	SO:0001067	H2BK5_monomethylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3011589	SO:0001714	SO:0000001	H2BK5_monomethylation_site	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	SO	2082144	SO:0001715	SO:0001411	ISRE	SO:0000001
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	2082145	SO:0001716	SO:0100021	histone_ubiqitination_site	SO:0000839
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	2082146	SO:0001717	SO:0001067	H2B_ubiquitination_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	3011590	SO:0001717	SO:0000001	H2B_ubiquitination_site	SO:0000110
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2082148	SO:0001718	SO:0100001	H3K18_acetylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	3056761	SO:0001718	SO:0001411	H3K18_acetylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2082150	SO:0001719	SO:0100001	H3K23_acylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	3056762	SO:0001719	SO:0001411	H3K23_acylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2082152	SO:0001721	SO:0100001	H3K27_acylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	3056763	SO:0001721	SO:0001411	H3K27_acylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2082154	SO:0001722	SO:0100001	H3K36_monomethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	3056764	SO:0001722	SO:0001411	H3K36_monomethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	2082156	SO:0001723	SO:0100001	H3K36_dimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	3056765	SO:0001723	SO:0001411	H3K36_dimethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	2082158	SO:0001724	SO:0100001	H3K36_trimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	3056766	SO:0001724	SO:0001411	H3K36_trimethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2082160	SO:0001725	SO:0100001	H3K4_dimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	3056767	SO:0001725	SO:0001411	H3K4_dimethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2082162	SO:0001726	SO:0100001	H3K27_dimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	3056768	SO:0001726	SO:0001411	H3K27_dimethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2082164	SO:0001727	SO:0100001	H3K9_monomethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	3056769	SO:0001727	SO:0001411	H3K9_monomethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	2082166	SO:0001728	SO:0100001	H3K9_dimethylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	3056770	SO:0001728	SO:0001411	H3K9_dimethylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2082168	SO:0001729	SO:0100001	H4K16_acylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	3056771	SO:0001729	SO:0001411	H4K16_acylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2082170	SO:0001730	SO:0100001	H4K5_acylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	3056772	SO:0001730	SO:0001411	H4K5_acylation_site	SO:0000001
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	2082172	SO:0001731	SO:0100001	H4K8_acylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	3056773	SO:0001731	SO:0001411	H4K8_acylation_site	SO:0000001
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2082174	SO:0001732	SO:0001067	H3K27_methylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	3011591	SO:0001732	SO:0000001	H3K27_methylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2082176	SO:0001733	SO:0001067	H3K36_methylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	3011592	SO:0001733	SO:0000001	H3K36_methylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	2082178	SO:0001734	SO:0001067	H3K4_methylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	3011593	SO:0001734	SO:0000001	H3K4_methylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2082180	SO:0001735	SO:0001067	H3K79_methylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	3011594	SO:0001735	SO:0000001	H3K79_methylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2082182	SO:0001736	SO:0001067	H3K9_methylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	3011595	SO:0001736	SO:0000001	H3K9_methylation_site	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	2082184	SO:0001737	SO:0100021	histone_acylation_region	SO:0000839
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	2082185	SO:0001738	SO:0001067	H4K_acylation_region	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	3011596	SO:0001738	SO:0000001	H4K_acylation_region	SO:0000110
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082187	SO:0001748	SO:0000835	SL3_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082188	SO:0001748	SO:0000835	SL3_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082189	SO:0001749	SO:0000835	SL4_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082190	SO:0001749	SO:0000835	SL4_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082191	SO:0001750	SO:0000835	SL5_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082192	SO:0001750	SO:0000835	SL5_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082193	SO:0001751	SO:0000835	SL6_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082194	SO:0001751	SO:0000835	SL6_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082195	SO:0001752	SO:0000835	SL7_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082196	SO:0001752	SO:0000835	SL7_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082197	SO:0001753	SO:0000835	SL8_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082198	SO:0001753	SO:0000835	SL8_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082199	SO:0001754	SO:0000835	SL9_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082200	SO:0001754	SO:0000835	SL9_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082201	SO:0001755	SO:0000835	SL10_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082202	SO:0001755	SO:0000835	SL10_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082203	SO:0001756	SO:0000835	SL11_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082204	SO:0001756	SO:0000835	SL11_acceptor_site	SO:0000833
6	"A transcript that in its initial state requires modification to be functional." [SO:ma]	\N	primary_transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082205	SO:0001757	SO:0000835	SL12_acceptor_site	SO:0000185
6	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2082206	SO:0001757	SO:0000835	SL12_acceptor_site	SO:0000833
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	2082207	SO:0001787	SO:0001878	splice_donor_5th_base_variant	SO:0001537
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	2082208	SO:0001788	SO:0001037	U_box	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	2082209	SO:0001788	SO:0001037	U_box	SO:0001411
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]	SO	2082210	SO:0001792	SO:0001537	non_coding_transcript_exon_variant	SO:0001060
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	2082214	SO:0001794	SO:0001235	point_centromere	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]	SO	2548856	SO:0001794	SO:0000001	point_centromere	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	2082216	SO:0001795	SO:0001235	regional_centromere	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]	SO	2548857	SO:0001795	SO:0000001	regional_centromere	SO:0000110
6	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	2082218	SO:0001796	SO:0000340	regional_centromere_central_core	SO:0001235
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	2706970	SO:0001796	SO:0001411	regional_centromere_central_core	SO:0000001
6	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	2082220	SO:0001798	SO:0000830	regional_centromere_inner_repeat_region	SO:0000340
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	2082221	SO:0001798	SO:0000830	regional_centromere_inner_repeat_region	SO:0001411
6	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	2082222	SO:0001799	SO:0000340	regional_centromere_outer_repeat_region	SO:0001235
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	SO	2082224	SO:0001800	SO:0001411	tasiRNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a tasiRNA." [PMID:16145017]	SO	2082225	SO:0001801	SO:0001411	tasiRNA_primary_transcript	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	2917111	SO:0001804	SO:0000001	DDB_box	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	2082227	SO:0001804	SO:0100021	DDB_box	SO:0000839
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	2082228	SO:0001805	SO:0000104	destruction_box	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	2441862	SO:0001805	SO:0001411	destruction_box	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	2082230	SO:0001807	SO:0000104	KEN_box	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	2441864	SO:0001807	SO:0001411	KEN_box	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	SO	2764393	SO:0001809	SO:0000001	signal_anchor	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	2917112	SO:0001810	SO:0000001	PIP_box	SO:0000110
6	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	2082236	SO:0001810	SO:0100021	PIP_box	SO:0000839
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	2082237	SO:0001811	SO:0000839	phosphorylation_site	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	2082238	SO:0001811	SO:0000839	phosphorylation_site	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	2279478	SO:0001812	SO:0000104	transmembrane_helix	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	2625397	SO:0001812	SO:0001411	transmembrane_helix	SO:0000001
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	2082241	SO:0001818	SO:0001878	protein_altering_variant	SO:0001537
6	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	2082242	SO:0001819	SO:0001878	synonymous_variant	SO:0001537
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	2082243	SO:0001820	SO:0001576	inframe_indel	SO:0001564
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	2082244	SO:0001821	SO:0001791	inframe_insertion	SO:0001576
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	2082245	SO:0001821	SO:0001968	inframe_insertion	SO:0001576
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	2082246	SO:0001822	SO:0001791	inframe_deletion	SO:0001576
6	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	2082247	SO:0001822	SO:0001968	inframe_deletion	SO:0001576
6	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	2082248	SO:0001823	SO:0001580	conservative_inframe_insertion	SO:0001791
6	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	2082249	SO:0001823	SO:0001580	conservative_inframe_insertion	SO:0001968
11	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	3011597	SO:0001823	SO:0001537	conservative_inframe_insertion	SO:0001060
6	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	2082251	SO:0001824	SO:0001580	disruptive_inframe_insertion	SO:0001791
6	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	2082252	SO:0001824	SO:0001580	disruptive_inframe_insertion	SO:0001968
11	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	3011598	SO:0001824	SO:0001537	disruptive_inframe_insertion	SO:0001060
6	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	2082254	SO:0001825	SO:0001580	conservative_inframe_deletion	SO:0001791
6	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	2082255	SO:0001825	SO:0001580	conservative_inframe_deletion	SO:0001968
6	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	2082256	SO:0001826	SO:0001580	disruptive_inframe_deletion	SO:0001791
6	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	2082257	SO:0001826	SO:0001580	disruptive_inframe_deletion	SO:0001968
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	2082264	SO:0001835	SO:0000298	N_region	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	2082265	SO:0001836	SO:0000298	S_region	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	SO	2082266	SO:0001839	SO:0001411	CSL_response_element	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	2082267	SO:0001840	SO:0001683	GATA_box	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	SO	2082268	SO:0001842	SO:0001411	AP_1_binding_site	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	SO	2082269	SO:0001843	SO:0001411	CRE	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	SO	2082270	SO:0001844	SO:0001411	CuRE	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	SO	2082271	SO:0001845	SO:0001411	DRE	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	SO	2082272	SO:0001846	SO:0001411	FLEX_element	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	SO	2082273	SO:0001847	SO:0001411	forkhead_motif	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	2082274	SO:0001848	SO:0001683	homol_D_box	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	SO	2082275	SO:0001849	SO:0001411	homol_E_box	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	SO	2082276	SO:0001850	SO:0001411	HSE	SO:0000001
6	"A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]	\N	sequence_motif	SOFA	SOFA	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	2082277	SO:0001851	SO:0000714	iron_repressed_GATA_element	SO:0001683
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	SO	2082278	SO:0001852	SO:0001411	mating_type_M_box	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]	SO	2082279	SO:0001853	SO:0000001	androgen_response_element	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]	SO	2082280	SO:0001854	SO:0000001	smFISH_probe	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	SO	2082281	SO:0001855	SO:0001411	MCB	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	SO	2082282	SO:0001856	SO:0001411	CCAAT_motif	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	SO	2082283	SO:0001857	SO:0001411	Ace2_UAS	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	SO	2082284	SO:0001858	SO:0001411	TR_box	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	SO	2082285	SO:0001859	SO:0001411	STREP_motif	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]	SO	2082286	SO:0001860	SO:0000001	rDNA_intergenic_spacer_element	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	SO	2082287	SO:0001861	SO:0001411	sterol_regulatory_element	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	2082288	SO:0001862	SO:0000657	GT_dinucleotide_repeat	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	2082289	SO:0001863	SO:0000657	GTT_trinucleotide_repeat	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]	SO	2082290	SO:0001864	SO:0000001	Sap1_recognition_motif	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	SO	2082291	SO:0001865	SO:0001411	CDRE_motif	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A contig of BAC reads." [GMOD:ea]	SO	2082292	SO:0001866	SO:0001409	BAC_read_contig	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	SO	2082293	SO:0001870	SO:0001411	enhancerRNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	SO	2082294	SO:0001871	SO:0001411	PCB	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	2279482	SO:0001875	SO:0001410	unassigned_supercontig	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	SO	2082296	SO:0001877	SO:0001411	lnc_RNA	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	2082297	SO:0001896	SO:0000673	transposable_element_CDS	SO:0000831
6	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2082300	SO:0001898	SO:0000830	dg_repeat	SO:0000340
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2082301	SO:0001898	SO:0000830	dg_repeat	SO:0001411
6	"Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]	\N	chromosome	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2082302	SO:0001899	SO:0000830	dh_repeat	SO:0000340
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2082303	SO:0001899	SO:0000830	dh_repeat	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]	SO	2082304	SO:0001900	SO:0000001	M26_binding_site	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	2082305	SO:0001901	SO:0001683	AACCCT_box	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	2082306	SO:0001903	SO:0000831	intronic_lncRNA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	2082307	SO:0001904	SO:0000831	antisense_lncRNA	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]	SO	2082308	SO:0001905	SO:0000001	regional_centromere_outer_repeat_transcript	SO:0000110
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	2082309	SO:0001909	SO:0001576	frameshift_elongation	SO:0001564
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	2082310	SO:0001910	SO:0001576	frameshift_truncation	SO:0001564
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	2548862	SO:0001913	SO:0000831	bacterial_RNApol_promoter_sigma_ecf	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]	SO	2082313	SO:0001914	SO:0000001	rDNA_replication_fork_barrier	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]	SO	2082314	SO:0001916	SO:0000001	CAGE_tag	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	2082315	SO:0001918	SO:0001411	5_methylcytosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	2082316	SO:0001919	SO:0001411	4_methylcytosine	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	2082317	SO:0001920	SO:0001411	N6_methyladenine	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	2279484	SO:0001922	SO:0001410	mitochondrial_supercontig	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	2082319	SO:0001923	SO:0000831	TERRA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	2082320	SO:0001924	SO:0000831	ARRET	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	2082321	SO:0001925	SO:0000831	ARIA	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	2082322	SO:0001926	SO:0000831	anti_ARRET	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	SO	2082323	SO:0001927	SO:0001411	telomeric_transcript	SO:0000001
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	2082330	SO:0001935	SO:0001067	H3K20_trimethylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	3011599	SO:0001935	SO:0000001	H3K20_trimethylation_site	SO:0000110
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	2082332	SO:0001936	SO:0100001	H3K36_acetylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	3056774	SO:0001936	SO:0001411	H3K36_acetylation_site	SO:0000001
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	2082334	SO:0001937	SO:0001067	H2BK12_acetylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	3011600	SO:0001937	SO:0000001	H2BK12_acetylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2082336	SO:0001938	SO:0001067	H2AK5_acetylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	3011601	SO:0001938	SO:0000001	H2AK5_acetylation_site	SO:0000110
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2082338	SO:0001939	SO:0100001	H4K12_acetylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	3056775	SO:0001939	SO:0001411	H4K12_acetylation_site	SO:0000001
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2082340	SO:0001940	SO:0001067	H2BK120_acetylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	3011602	SO:0001940	SO:0000001	H2BK120_acetylation_site	SO:0000110
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2082342	SO:0001941	SO:0100001	H4K91_acetylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	3056776	SO:0001941	SO:0001411	H4K91_acetylation_site	SO:0000001
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2082344	SO:0001942	SO:0001067	H2BK20_acetylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	3011603	SO:0001942	SO:0000001	H2BK20_acetylation_site	SO:0000110
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2082346	SO:0001943	SO:0100001	H3K4ac_acetylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	3056777	SO:0001943	SO:0001411	H3K4ac_acetylation_site	SO:0000001
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2082348	SO:0001944	SO:0001067	H2AK9_acetylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	3011604	SO:0001944	SO:0000001	H2AK9_acetylation_site	SO:0000110
6	"A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]	\N	polypeptide_motif	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2082350	SO:0001945	SO:0100001	H3K56_acetylation_site	SO:0001067
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	3056778	SO:0001945	SO:0001411	H3K56_acetylation_site	SO:0000001
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2082352	SO:0001946	SO:0001067	H2BK15_acetylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	3011605	SO:0001946	SO:0000001	H2BK15_acetylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	2082354	SO:0001947	SO:0001067	H3R2_monomethylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	3011606	SO:0001947	SO:0000001	H3R2_monomethylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2082356	SO:0001948	SO:0001067	H3R2_dimethylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	3011607	SO:0001948	SO:0000001	H3R2_dimethylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	2082358	SO:0001949	SO:0001067	H4R3_dimethylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	3011608	SO:0001949	SO:0000001	H4R3_dimethylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	2082360	SO:0001950	SO:0001067	H4K4_trimethylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	3011609	SO:0001950	SO:0000001	H4K4_trimethylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2082362	SO:0001951	SO:0001067	H3K23_dimethylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	3011610	SO:0001951	SO:0000001	H3K23_dimethylation_site	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	SO	2082364	SO:0001952	SO:0001411	promoter_flanking_region	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	2082365	SO:0001958	SO:0000831	lariat_intron	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of intron whereby the excision is driven by lariat formation." [SO:ke]	SO	2548865	SO:0001958	SO:0000001	lariat_intron	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	2082367	SO:0001959	SO:0001683	TCT_motif	SO:0001411
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	2082368	SO:0001960	SO:0001411	5_hydroxymethylcytosine	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]	SO	2082369	SO:0001961	SO:0000001	5_formylcytosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	2082370	SO:0001965	SO:0000001	8_oxoguanine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]	SO	2082371	SO:0001966	SO:0000001	5_carboxylcytosine	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]	SO	2082372	SO:0001967	SO:0000001	8_oxoadenine	SO:0000110
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a coding transcript." [SO:ke]	SO	2082373	SO:0001969	SO:0001537	coding_transcript_intron_variant	SO:0001060
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant occurring within an intron of a non coding transcript." [SO:ke]	SO	2082374	SO:0001970	SO:0001537	non_coding_transcript_intron_variant	SO:0001060
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2082375	SO:0001971	SO:0000001	zinc_finger_binding_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2082376	SO:0001972	SO:0001067	histone_4_acylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	3011611	SO:0001972	SO:0000001	histone_4_acylation_site	SO:0000110
6	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2082378	SO:0001973	SO:0001067	histone_3_acetylation_site	SO:0100021
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	3011612	SO:0001973	SO:0000001	histone_3_acetylation_site	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	SO	2082380	SO:0001974	SO:0001411	CTCF_binding_site	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]	SO	2082381	SO:0001975	SO:0000001	five_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]	SO	2082382	SO:0001976	SO:0000001	three_prime_sticky_end_restriction_enzyme_cleavage_site	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A motif that affects the stability of RNA." [PMID:22495308, SO:ke]	SO	2082383	SO:0001979	SO:0000001	RNA_stability_element	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	2082384	SO:0001980	SO:0001683	G_box	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	2082385	SO:0001981	SO:0001683	L_box	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	2082386	SO:0001982	SO:0001683	I-box	SO:0001411
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	2082387	SO:0001983	SO:0001564	5_prime_UTR_premature_start_codon_variant	SO:0001878
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	2082388	SO:0001988	SO:0001576	5_prime_UTR_premature_start_codon_gain_variant	SO:0001564
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	2082389	SO:0001989	SO:0001576	5_prime_UTR_premature_start_codon_loss_variant	SO:0001564
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	2082390	SO:0001990	SO:0001576	five_prime_UTR_premature_start_codon_location_variant	SO:0001564
6	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	2082391	SO:0001992	SO:0001576	nonsynonymous_variant	SO:0001564
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	2082392	SO:0001993	SO:0000673	extended_cis_splice_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	2707048	SO:0001993	SO:0001411	extended_cis_splice_site	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	2548866	SO:0001994	SO:0000831	intron_base_5	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]	SO	2917127	SO:0001994	SO:0000001	intron_base_5	SO:0000110
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]	SO	2082396	SO:0001995	SO:0001537	extended_intronic_splice_region_variant	SO:0001060
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	2279489	SO:0001996	SO:0000831	extended_intronic_splice_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Region of intronic sequence within 10 bases of an exon." [SANGER:am]	SO	2764401	SO:0001996	SO:0000001	extended_intronic_splice_region	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]	SO	2279491	SO:0002000	SO:0000001	W_region	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]	SO	2279492	SO:0002001	SO:0000001	Y_region	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	2279493	SO:0002002	SO:0000001	Z1_region	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]	SO	2279494	SO:0002003	SO:0000001	Z2_region	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]	SO	2082408	SO:0002005	SO:0000001	DSR_motif	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	SO	2082409	SO:0002006	SO:0001411	zinc_repressed_element	SO:0000001
6	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2082410	SO:0002008	SO:0001818	rare_amino_acid_variant	SO:0001580
6	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2082411	SO:0002009	SO:0001650	selenocysteine_loss	SO:0001818
6	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	\N	protein_altering_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2082412	SO:0002010	SO:0001650	pyrrolysine_loss	SO:0001818
8	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	2548869	SO:0002012	SO:0001564	start_lost	SO:0001878
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	2082414	SO:0002013	SO:0001564	5_prime_UTR_truncation	SO:0001878
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	2082415	SO:0002014	SO:0001564	5_prime_UTR_elongation	SO:0001878
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	2082416	SO:0002015	SO:0001564	3_prime_UTR_truncation	SO:0001878
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	2082417	SO:0002016	SO:0001564	3_prime_UTR_elongation	SO:0001878
6	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A transcript variant occurring within a conserved region of an intron." [SO:ke]	SO	2082418	SO:0002018	SO:0001537	conserved_intron_variant	SO:0001060
6	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	2082419	SO:0002019	SO:0001564	start_retained_variant	SO:0001878
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]	SO	2082420	SO:0002020	SO:0000001	boundary_element	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]	SO	2082421	SO:0002021	SO:0000001	mating_type_region_replication_fork_barrier	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	SO	2082422	SO:0002022	SO:0001411	priRNA	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]	SO	2082423	SO:0002023	SO:0000001	multiplexing_sequence_identifier	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"One of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	2279495	SO:0002024	SO:0000001	W_region	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	SO	2082426	SO:0002025	SO:0000001	cis_acting_homologous_chromosome_pairing_region	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"One of two segments of homology found at all\\nthree mating loci (HML, MAT, and HMR)." [SGD:jd]	SO	2279496	SO:0002030	SO:0000001	X_region	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	SO	2082429	SO:0002031	SO:0001411	shRNA	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	2082430	SO:0005837	SO:0000831	U14_snoRNA_primary_transcript	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	2082431	SO:0005841	SO:0000673	methylation_guide_snoRNA	SO:0000831
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	SO	2082432	SO:0005843	SO:0001411	rRNA_cleavage_RNA	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2082434	SO:0005850	SO:0001037	primer_binding_site	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2082435	SO:0005850	SO:0001037	primer_binding_site	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	2082436	SO:0005856	SO:0000831	selenocysteine_tRNA_primary_transcript	SO:0001411
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	2082437	SO:0005857	SO:0000831	selenocysteinyl_tRNA	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]	SO	2279497	SO:0100001	SO:0000001	biochemical_region_of_peptide	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	2082440	SO:0100002	SO:0000104	molecular_contact_region	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	2441993	SO:0100002	SO:0001411	molecular_contact_region	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279498	SO:0100004	SO:0000001	catmat_left_handed_three	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279499	SO:0100005	SO:0000001	catmat_left_handed_four	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279500	SO:0100006	SO:0000001	catmat_right_handed_three	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279501	SO:0100007	SO:0000001	catmat_right_handed_four	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2279502	SO:0100008	SO:0000001	alpha_beta_motif	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]	SO	2279503	SO:0100012	SO:0000001	peptide_coil	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	SO	2279504	SO:0100017	SO:0000001	polypeptide_conserved_motif	SO:0000110
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	2082456	SO:0100018	SO:0000104	polypeptide_binding_motif	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	2441995	SO:0100018	SO:0001411	polypeptide_binding_motif	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	2082458	SO:0100019	SO:0000104	polypeptide_catalytic_motif	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	2441997	SO:0100019	SO:0001411	polypeptide_catalytic_motif	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	2764402	SO:0100020	SO:0000001	polypeptide_DNA_contact	SO:0000110
6	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	2082461	SO:0100020	SO:0000839	polypeptide_DNA_contact	SO:0000104
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	2082462	SO:0100020	SO:0000839	polypeptide_DNA_contact	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]	SO	2082463	SO:1000010	SO:0000001	pyrimidine_transition	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	2082464	SO:1000011	SO:0001059	C_to_T_transition	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	2082465	SO:1000011	SO:0001411	C_to_T_transition	SO:0000001
6	"A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]	\N	sequence_alteration	SOFA	SOFA	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	2082466	SO:1000012	SO:1000002	C_to_T_transition_at_pCpG_site	SO:0001059
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	2082467	SO:1000012	SO:1000002	C_to_T_transition_at_pCpG_site	SO:0001411
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2082468	SO:1000013	SO:0001059	T_to_C_transition	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2082469	SO:1000013	SO:0001411	T_to_C_transition	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A substitution of a purine, A or G, for another purine." [SO:ke]	SO	2082470	SO:1000014	SO:0000001	purine_transition	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	2082471	SO:1000015	SO:0001059	A_to_G_transition	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	2082472	SO:1000015	SO:0001411	A_to_G_transition	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	2082473	SO:1000016	SO:0001059	G_to_A_transition	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	2082474	SO:1000016	SO:0001411	G_to_A_transition	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]	SO	2082475	SO:1000018	SO:0000001	pyrimidine_to_purine_transversion	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	2082476	SO:1000019	SO:0001059	C_to_A_transversion	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	2082477	SO:1000019	SO:0001411	C_to_A_transversion	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2082478	SO:1000020	SO:0001059	C_to_G_transversion	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2082479	SO:1000020	SO:0001411	C_to_G_transversion	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from T to A." [SO:ke]	SO	2082480	SO:1000021	SO:0001059	T_to_A_transversion	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transversion from T to A." [SO:ke]	SO	2082481	SO:1000021	SO:0001411	T_to_A_transversion	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from T to G." [SO:ke]	SO	2082482	SO:1000022	SO:0001059	T_to_G_transversion	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transversion from T to G." [SO:ke]	SO	2082483	SO:1000022	SO:0001411	T_to_G_transversion	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]	SO	2082484	SO:1000023	SO:0000001	purine_to_pyrimidine_transversion	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	2082485	SO:1000024	SO:0001059	A_to_C_transversion	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	2082486	SO:1000024	SO:0001411	A_to_C_transversion	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	2082487	SO:1000025	SO:0001059	A_to_T_transversion	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	2082488	SO:1000025	SO:0001411	A_to_T_transversion	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	2082489	SO:1000026	SO:0001059	G_to_C_transversion	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	2082490	SO:1000026	SO:0001411	G_to_C_transversion	SO:0000001
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	2082491	SO:1000027	SO:0001059	G_to_T_transversion	SO:0000110
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	2082492	SO:1000027	SO:0001411	G_to_T_transversion	SO:0000001
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal structure variation within a single chromosome." [SO:ke]	SO	2082493	SO:1000028	SO:0001026	intrachromosomal_mutation	SO:0001260
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	2082494	SO:1000029	SO:0001506	chromosomal_deletion	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	2082495	SO:1000030	SO:0001506	chromosomal_inversion	SO:0001026
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]	SO	2082496	SO:1000031	SO:0001026	interchromosomal_mutation	SO:0001260
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An extra chromosome." [SO:ke]	SO	2082497	SO:1000037	SO:0001026	chromosomal_duplication	SO:0001260
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	2082498	SO:1000038	SO:0001506	intrachromosomal_duplication	SO:0001026
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tandem duplication where the individual regions are in the same orientation." [SO:ke]	SO	2082499	SO:1000039	SO:0000001	direct_tandem_duplication	SO:0000110
6	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tandem duplication where the individual regions are not in the same orientation." [SO:ke]	SO	2082500	SO:1000040	SO:0000001	inverted_tandem_duplication	SO:0000110
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	2279505	SO:1000041	SO:0001506	intrachromosomal_transposition	SO:0001026
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]	SO	2082502	SO:1000042	SO:0001026	compound_chromosome	SO:0001260
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	2082503	SO:1000043	SO:0001507	Robertsonian_fusion	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	2082504	SO:1000043	SO:0001524	Robertsonian_fusion	SO:0001506
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	2082505	SO:1000044	SO:0001506	chromosomal_translocation	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	2082506	SO:1000045	SO:0001506	ring_chromosome	SO:0001026
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	2082507	SO:1000046	SO:0001507	pericentric_inversion	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	2082508	SO:1000046	SO:0001524	pericentric_inversion	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	2082509	SO:1000047	SO:0001507	paracentric_inversion	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	2082510	SO:1000047	SO:0001524	paracentric_inversion	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	2082511	SO:1000048	SO:0001507	reciprocal_chromosomal_translocation	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	2082512	SO:1000048	SO:0001524	reciprocal_chromosomal_translocation	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]	SO	2082513	SO:1000136	SO:0001026	autosynaptic_chromosome	SO:0001260
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	2082514	SO:1000138	SO:0001506	homo_compound_chromosome	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	2082515	SO:1000140	SO:0001506	hetero_compound_chromosome	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	2082516	SO:1000141	SO:0001506	chromosome_fission	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	2082517	SO:1000142	SO:0001506	dexstrosynaptic_chromosome	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	2082518	SO:1000143	SO:0001506	laevosynaptic_chromosome	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	2082519	SO:1000144	SO:0001506	free_duplication	SO:0001026
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	2082520	SO:1000145	SO:0001507	free_ring_duplication	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	2082521	SO:1000145	SO:0001524	free_ring_duplication	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variant with 4 or more breakpoints." [FB:reference_manual, SO:ke]	SO	2082522	SO:1000146	SO:0001026	complex_chromosomal_mutation	SO:0001260
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	2082523	SO:1000147	SO:0001507	deficient_translocation	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	2082524	SO:1000147	SO:0001524	deficient_translocation	SO:0001506
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	2279506	SO:1000148	SO:0001506	inversion_cum_translocation	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	2279507	SO:1000149	SO:0001506	bipartite_duplication	SO:0001026
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	2082527	SO:1000150	SO:0001507	cyclic_translocation	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	2082528	SO:1000150	SO:0001524	cyclic_translocation	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	2082529	SO:1000151	SO:0001507	bipartite_inversion	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	2082530	SO:1000151	SO:0001524	bipartite_inversion	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2082531	SO:1000152	SO:0001507	uninverted_insertional_duplication	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2082532	SO:1000152	SO:0001524	uninverted_insertional_duplication	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	2082533	SO:1000153	SO:0001507	inverted_insertional_duplication	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	2082534	SO:1000153	SO:0001524	inverted_insertional_duplication	SO:0001506
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	2082535	SO:1000154	SO:0001506	insertional_duplication	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	2082536	SO:1000155	SO:0001506	interchromosomal_transposition	SO:0001026
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	2082537	SO:1000156	SO:0001507	inverted_interchromosomal_transposition	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	2082538	SO:1000156	SO:0001524	inverted_interchromosomal_transposition	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2082539	SO:1000157	SO:0001507	uninverted_interchromosomal_transposition	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2082540	SO:1000157	SO:0001524	uninverted_interchromosomal_transposition	SO:0001506
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	2279508	SO:1000158	SO:0001507	inverted_intrachromosomal_transposition	SO:0001260
7	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	2279509	SO:1000158	SO:0001524	inverted_intrachromosomal_transposition	SO:0001506
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2279510	SO:1000159	SO:0001507	uninverted_intrachromosomal_transposition	SO:0001260
7	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2279511	SO:1000159	SO:0001524	uninverted_intrachromosomal_transposition	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2082545	SO:1000160	SO:0001507	unoriented_insertional_duplication	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2082546	SO:1000160	SO:0001524	unoriented_insertional_duplication	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2082547	SO:1000161	SO:0001507	unoriented_interchromosomal_transposition	SO:0001260
6	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2082548	SO:1000161	SO:0001524	unoriented_interchromosomal_transposition	SO:0001506
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2279512	SO:1000162	SO:0001507	unoriented_intrachromosomal_transposition	SO:0001260
7	"A collection of sequences (often chromosomes) of an individual." [SO:ke]	\N	variant_genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2279513	SO:1000162	SO:0001524	unoriented_intrachromosomal_transposition	SO:0001506
6	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	2082551	SO:1000170	SO:0001026	uncharacterised_chromosomal_mutation	SO:0001260
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	2279514	SO:1000171	SO:0001506	deficient_inversion	SO:0001026
6	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"" []	SO	2082553	SO:1000175	SO:0001506	partially_characterised_chromosomal_mutation	SO:0001026
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]	SO	2082554	SO:1001190	SO:0000733	encodes_different_polypeptides_different_stop	SO:0000400
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]	SO	2082555	SO:1001191	SO:0000733	encodes_overlapping_peptides_different_start	SO:0000400
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]	SO	2082556	SO:1001193	SO:0000733	encodes_overlapping_polypeptides_different_start_and_stop	SO:0000400
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript that has the quality dicistronic." [SO:xp]	SO	2279515	SO:1001197	SO:0000001	dicistronic_primary_transcript	SO:0000110
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	2082558	SO:1001246	SO:0000673	CDS_independently_known	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	2707084	SO:1001246	SO:0001411	CDS_independently_known	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	2082560	SO:1001247	SO:0000233	orphan_CDS	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	2082561	SO:1001247	SO:0000833	orphan_CDS	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	2082562	SO:1001247	SO:0000833	orphan_CDS	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	2279516	SO:1001249	SO:0000233	CDS_supported_by_domain_match_data	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	2279517	SO:1001249	SO:0000833	CDS_supported_by_domain_match_data	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	2279518	SO:1001249	SO:0000833	CDS_supported_by_domain_match_data	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	2279519	SO:1001251	SO:0000673	CDS_supported_by_sequence_similarity_data	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	2848930	SO:1001251	SO:0001411	CDS_supported_by_sequence_similarity_data	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	2082568	SO:1001254	SO:0000673	CDS_predicted	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	2707090	SO:1001254	SO:0001411	CDS_predicted	SO:0000001
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	2279521	SO:1001259	SO:0000233	CDS_supported_by_EST_or_cDNA_data	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	2279522	SO:1001259	SO:0000833	CDS_supported_by_EST_or_cDNA_data	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	2279523	SO:1001259	SO:0000833	CDS_supported_by_EST_or_cDNA_data	SO:0001411
9	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2764403	SO:1001260	SO:0000673	internal_Shine_Dalgarno_sequence	SO:0000831
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	3034774	SO:1001260	SO:0001411	internal_Shine_Dalgarno_sequence	SO:0000001
6	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	2082577	SO:1001261	SO:0001411	recoded_mRNA	SO:0000001
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a translational frameshift of -1." [SO:ke]	SO	2082578	SO:1001262	SO:0000733	minus_1_translationally_frameshifted	SO:0000400
6	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing a translational frameshift of +1." [SO:ke]	SO	2082579	SO:1001263	SO:0000733	plus_1_translationally_frameshifted	SO:0000400
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	2279526	SO:1001264	SO:0001411	mRNA_recoded_by_translational_bypass	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	2279527	SO:1001265	SO:0001411	mRNA_recoded_by_codon_redefinition	SO:0000001
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	2082582	SO:1001268	SO:0000831	recoding_stimulatory_region	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	SO	2548871	SO:1001268	SO:0000001	recoding_stimulatory_region	SO:0000110
6	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2082584	SO:1001269	SO:0000316	four_bp_start_codon	SO:0000836
7	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2442068	SO:1001269	SO:0000836	four_bp_start_codon	SO:0000234
7	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2442069	SO:1001269	SO:0000836	four_bp_start_codon	SO:0000834
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	2082587	SO:1001271	SO:0000673	archaeal_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	2707097	SO:1001271	SO:0001411	archaeal_intron	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	2082589	SO:1001272	SO:0000673	tRNA_intron	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	2707098	SO:1001272	SO:0001411	tRNA_intron	SO:0000001
6	"A region of an mRNA." [SO:cb]	\N	mRNA_region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2082591	SO:1001273	SO:0000316	CTG_start_codon	SO:0000836
7	"Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]	\N	mRNA	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2442076	SO:1001273	SO:0000836	CTG_start_codon	SO:0000234
7	"A region of a mature transcript." [SO:ke]	\N	mature_transcript_region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2442077	SO:1001273	SO:0000836	CTG_start_codon	SO:0000834
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	2082594	SO:1001274	SO:0000673	SECIS_element	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	2707102	SO:1001274	SO:0001411	SECIS_element	SO:0000001
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	2082596	SO:1001277	SO:0000673	three_prime_recoding_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	2707103	SO:1001277	SO:0001411	three_prime_recoding_site	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	2082598	SO:1001279	SO:0000233	three_prime_stem_loop_structure	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	2082599	SO:1001279	SO:0000833	three_prime_stem_loop_structure	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	2082600	SO:1001279	SO:0000833	three_prime_stem_loop_structure	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	2082601	SO:1001280	SO:0000673	five_prime_recoding_site	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	2707106	SO:1001280	SO:0001411	five_prime_recoding_site	SO:0000001
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	2082603	SO:1001281	SO:0000233	flanking_three_prime_quadruplet_recoding_signal	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	2082604	SO:1001281	SO:0000833	flanking_three_prime_quadruplet_recoding_signal	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	2082605	SO:1001281	SO:0000833	flanking_three_prime_quadruplet_recoding_signal	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	2082606	SO:1001282	SO:0000233	UAG_stop_codon_signal	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	2082607	SO:1001282	SO:0000833	UAG_stop_codon_signal	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	2082608	SO:1001282	SO:0000833	UAG_stop_codon_signal	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	2082609	SO:1001283	SO:0000233	UAA_stop_codon_signal	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	2082610	SO:1001283	SO:0000833	UAA_stop_codon_signal	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	2082611	SO:1001283	SO:0000833	UAA_stop_codon_signal	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	2082612	SO:1001285	SO:0000233	UGA_stop_codon_signal	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	2082613	SO:1001285	SO:0000833	UGA_stop_codon_signal	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	2082614	SO:1001285	SO:0000833	UGA_stop_codon_signal	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	2082615	SO:1001286	SO:0000233	three_prime_repeat_recoding_signal	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	2082616	SO:1001286	SO:0000833	three_prime_repeat_recoding_signal	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	2082617	SO:1001286	SO:0000833	three_prime_repeat_recoding_signal	SO:0001411
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	2082618	SO:1001287	SO:0000233	distant_three_prime_recoding_signal	SO:0000673
6	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	2082619	SO:1001287	SO:0000833	distant_three_prime_recoding_signal	SO:0000673
6	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	2082620	SO:1001287	SO:0000833	distant_three_prime_recoding_signal	SO:0001411
6	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	2082621	SO:1001288	SO:0000673	stop_codon_signal	SO:0000831
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	2707119	SO:1001288	SO:0001411	stop_codon_signal	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	SO	2441013	SO:0000012	SO:0000001	scRNA_primary_transcript	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A small non coding RNA sequence, present in the cytoplasm." [SO:ke]	SO	2441014	SO:0000013	SO:0000001	scRNA	SO:0000110
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	2995340	SO:0000014	SO:0001411	INR_motif	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	2441016	SO:0000014	SO:0001679	INR_motif	SO:0005836
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	2995341	SO:0000015	SO:0001411	DPE_motif	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	2441018	SO:0000015	SO:0001679	DPE_motif	SO:0005836
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	2995342	SO:0000016	SO:0001411	BREu_motif	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	2441020	SO:0000016	SO:0001679	BREu_motif	SO:0005836
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]	SO	2441022	SO:0000021	SO:0000001	asymmetric_RNA_internal_loop	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	2441023	SO:0000023	SO:0001411	K_turn_RNA_motif	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	2441024	SO:0000024	SO:0001411	sarcin_like_RNA_motif	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]	SO	2441025	SO:0000025	SO:0000001	symmetric_RNA_internal_loop	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441026	SO:0000027	SO:0000001	RNA_hook_turn	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	2441027	SO:0000037	SO:0001411	locus_control_region	SO:0000001
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]	SO	2441028	SO:0000055	SO:0001026	hyperploid	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]	SO	2441029	SO:0000056	SO:0001026	hypoploid	SO:0001260
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]	SO	2441030	SO:0000057	SO:0000001	operator	SO:0000110
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	2441031	SO:0000060	SO:0001026	compound_chromosome_arm	SO:0001260
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]	SO	2441032	SO:0000061	SO:0000001	restriction_enzyme_binding_site	SO:0000110
8	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	2625323	SO:0000062	SO:0001506	deficient_intrachromosomal_transposition	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	2441034	SO:0000063	SO:0001506	deficient_interchromosomal_transposition	SO:0001026
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441035	SO:0000107	SO:0000001	sequencing_primer	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA with a frameshift." [SO:xp]	SO	2441036	SO:0000108	SO:0000001	mRNA_with_frameshift	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	2441037	SO:0000121	SO:0000001	forward_primer	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	2441038	SO:0000132	SO:0000001	reverse_primer	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	2625324	SO:0000145	SO:0000673	recoded_codon	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	2981281	SO:0000145	SO:0001411	recoded_codon	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	2441041	SO:0000163	SO:0000831	five_prime_cis_splice_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	2806601	SO:0000163	SO:0000001	five_prime_cis_splice_site	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	2441043	SO:0000164	SO:0000831	three_prime_cis_splice_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	SO	2806602	SO:0000164	SO:0000001	three_prime_cis_splice_site	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441045	SO:0000165	SO:0001411	enhancer	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An enhancer bound by a factor." [SO:xp]	SO	2441046	SO:0000166	SO:0000831	enhancer_bound_by_factor	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]	SO	2441047	SO:0000167	SO:0000001	promoter	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	2441048	SO:0000169	SO:0000831	RNApol_I_promoter	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	2441049	SO:0000170	SO:0000831	RNApol_II_promoter	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	2441050	SO:0000171	SO:0000831	RNApol_III_promoter	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441051	SO:0000172	SO:0005836	CAAT_signal	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2939574	SO:0000173	SO:0000001	GC_rich_promoter_region	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441053	SO:0000173	SO:0005836	GC_rich_promoter_region	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	2441054	SO:0000174	SO:0001411	TATA_box	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2806603	SO:0000175	SO:0000831	minus_10_signal	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2806604	SO:0000176	SO:0000831	minus_35_signal	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	2441059	SO:0000184	SO:0000831	U2_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]	SO	2806605	SO:0000184	SO:0000001	U2_intron	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	2706475	SO:0000194	SO:0000001	LINE_element	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	SO	2441067	SO:0000194	SO:0001411	LINE_element	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441073	SO:0000204	SO:0000831	five_prime_UTR	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2806606	SO:0000204	SO:0000001	five_prime_UTR	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2441075	SO:0000205	SO:0000831	three_prime_UTR	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2806607	SO:0000205	SO:0000001	three_prime_UTR	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	2706478	SO:0000206	SO:0000001	SINE_element	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]	SO	2441078	SO:0000206	SO:0001411	SINE_element	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a ribosomal RNA." [SO:ke]	SO	2441080	SO:0000209	SO:0000001	rRNA_primary_transcript	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]	SO	2441081	SO:0000210	SO:0000001	tRNA_primary_transcript	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	2441082	SO:0000211	SO:0001411	alanine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	2441083	SO:0000212	SO:0001411	arginine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	2441084	SO:0000213	SO:0001411	asparagine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	2441085	SO:0000214	SO:0001411	aspartic_acid_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	2441086	SO:0000215	SO:0001411	cysteine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	2441087	SO:0000216	SO:0001411	glutamic_acid_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	2441088	SO:0000217	SO:0001411	glutamine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	2441089	SO:0000218	SO:0001411	glycine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	2441090	SO:0000219	SO:0001411	histidine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	2441091	SO:0000220	SO:0001411	isoleucine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	2441092	SO:0000221	SO:0001411	leucine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	2441093	SO:0000222	SO:0001411	lysine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	2441094	SO:0000223	SO:0001411	methionine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	2441095	SO:0000224	SO:0001411	phenylalanine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	2441096	SO:0000225	SO:0001411	proline_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	2441097	SO:0000226	SO:0001411	serine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	2441098	SO:0000227	SO:0001411	threonine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	2441099	SO:0000228	SO:0001411	tryptophan_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	2441100	SO:0000229	SO:0001411	tyrosine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	2441101	SO:0000230	SO:0001411	valine_tRNA_primary_transcript	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]	SO	2441102	SO:0000231	SO:0000001	snRNA_primary_transcript	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]	SO	2441103	SO:0000232	SO:0000001	snoRNA_primary_transcript	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	2441105	SO:0000241	SO:0000831	internal_UTR	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]	SO	2806608	SO:0000241	SO:0000001	internal_UTR	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	2441107	SO:0000242	SO:0000831	untranslated_region_polycistronic_mRNA	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]	SO	2806609	SO:0000242	SO:0000001	untranslated_region_polycistronic_mRNA	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	2806610	SO:0000243	SO:0000831	internal_ribosome_entry_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]	SO	3023301	SO:0000243	SO:0000001	internal_ribosome_entry_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]	SO	2441111	SO:0000252	SO:0000001	rRNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	SO	2441112	SO:0000253	SO:0000001	tRNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	2441113	SO:0000254	SO:0001411	alanyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	2441114	SO:0000255	SO:0001411	rRNA_small_subunit_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	2441115	SO:0000256	SO:0001411	asparaginyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	2441116	SO:0000257	SO:0001411	aspartyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	2441117	SO:0000258	SO:0001411	cysteinyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	2441118	SO:0000259	SO:0001411	glutaminyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	2441119	SO:0000260	SO:0001411	glutamyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	2441120	SO:0000261	SO:0001411	glycyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	2441121	SO:0000262	SO:0001411	histidyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	2441122	SO:0000263	SO:0001411	isoleucyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	2441123	SO:0000264	SO:0001411	leucyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	2441124	SO:0000265	SO:0001411	lysyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	2441125	SO:0000266	SO:0001411	methionyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	2441126	SO:0000267	SO:0001411	phenylalanyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	2441127	SO:0000268	SO:0001411	prolyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	2441128	SO:0000269	SO:0001411	seryl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	2441129	SO:0000270	SO:0001411	threonyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	2441130	SO:0000271	SO:0001411	tryptophanyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	2441131	SO:0000272	SO:0001411	tyrosyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	2441132	SO:0000273	SO:0001411	valyl_tRNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]	SO	2441133	SO:0000274	SO:0000001	snRNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]	SO	2441134	SO:0000275	SO:0000001	snoRNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	2441135	SO:0000276	SO:0001411	miRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	2441136	SO:0000282	SO:0001411	mRNA_with_minus_1_frameshift	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441139	SO:0000290	SO:0000001	dinucleotide_repeat_microsatellite_feature	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441140	SO:0000291	SO:0000001	trinucleotide_repeat_microsatellite_feature	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	2441141	SO:0000295	SO:0000831	U12_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]	SO	2806612	SO:0000295	SO:0000001	U12_intron	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441143	SO:0000301	SO:0000001	vertebrate_immune_system_gene_recombination_feature	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441144	SO:0000302	SO:0000298	J_gene_recombination_feature	SO:0001411
8	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	2625328	SO:0000318	SO:0000673	start_codon	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	2981282	SO:0000318	SO:0001411	start_codon	SO:0000001
8	"A region of a gene." [SO:ke]	SOFA	gene_member_region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	2625330	SO:0000319	SO:0000673	stop_codon	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	2981283	SO:0000319	SO:0001411	stop_codon	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	2441150	SO:0000321	SO:0001411	mRNA_with_plus_1_frameshift	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441151	SO:0000322	SO:0001411	nuclease_hypersensitive_site	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	2625332	SO:0000323	SO:0000831	coding_start	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The first base to be translated into protein." [SO:ke]	SO	2939575	SO:0000323	SO:0000001	coding_start	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	2441154	SO:0000325	SO:0001411	rRNA_large_subunit_primary_transcript	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	2625334	SO:0000327	SO:0000831	coding_end	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The last base to be translated into protein. It does not include the stop codon." [SO:ke]	SO	2939576	SO:0000327	SO:0000001	coding_end	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	2441157	SO:0000329	SO:0001411	mRNA_with_plus_2_frameshift	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	2441158	SO:0000335	SO:0001411	mRNA_with_minus_2_frameshift	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	2706536	SO:0000338	SO:0000001	MITE	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]	SO	2441160	SO:0000338	SO:0001411	MITE	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Region of a transcript that regulates splicing." [SO:ke]	SO	2441161	SO:0000344	SO:0000001	splice_enhancer	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441162	SO:0000346	SO:0001411	loxP_site	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	2441163	SO:0000350	SO:0001411	FRT_site	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	2441164	SO:0000354	SO:0001411	group_1_intron_homing_endonuclease_target_region	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	2625336	SO:0000360	SO:0000831	codon	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]	SO	2939577	SO:0000360	SO:0000001	codon	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]	SO	2441168	SO:0000370	SO:0000001	small_regulatory_ncRNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	2441170	SO:0000375	SO:0000831	rRNA_5_8S	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	2441171	SO:0000376	SO:0001411	RNA_6S	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	2441172	SO:0000377	SO:0001411	CsrB_RsmB_RNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	2441173	SO:0000378	SO:0001411	DsrA_RNA	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	2441174	SO:0000379	SO:0000831	GcvB_RNA	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2441175	SO:0000381	SO:0000673	group_IIA_intron	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885621	SO:0000381	SO:0001411	group_IIA_intron	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2441177	SO:0000382	SO:0000673	group_IIB_intron	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885622	SO:0000382	SO:0001411	group_IIB_intron	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	2441179	SO:0000383	SO:0001411	MicF_RNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	2441180	SO:0000384	SO:0001411	OxyS_RNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	SO	2441181	SO:0000385	SO:0000001	RNase_MRP_RNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	SO	2441182	SO:0000386	SO:0000001	RNase_P_RNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	2441183	SO:0000387	SO:0001411	RprA_RNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	2441184	SO:0000388	SO:0001411	RRE_RNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	2441185	SO:0000389	SO:0001411	spot_42_RNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	SO	2441186	SO:0000390	SO:0000001	telomerase_RNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	2441187	SO:0000391	SO:0001411	U1_snRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	2441188	SO:0000392	SO:0001411	U2_snRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	2441189	SO:0000393	SO:0001411	U4_snRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	2441190	SO:0000394	SO:0001411	U4atac_snRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	2441191	SO:0000395	SO:0001411	U5_snRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	2441192	SO:0000396	SO:0001411	U6_snRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	2441193	SO:0000397	SO:0001411	U6atac_snRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	2441194	SO:0000398	SO:0001411	U11_snRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	2441195	SO:0000399	SO:0001411	U12_snRNA	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	2441196	SO:0000403	SO:0000831	U14_snoRNA	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	SO	2441197	SO:0000404	SO:0000001	vault_RNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	SO	2441198	SO:0000405	SO:0000001	Y_RNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	2441200	SO:0000407	SO:0000831	rRNA_18S	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441201	SO:0000420	SO:0001037	five_prime_terminal_inverted_repeat	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2441202	SO:0000420	SO:0001037	five_prime_terminal_inverted_repeat	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441203	SO:0000421	SO:0001037	three_prime_terminal_inverted_repeat	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2441204	SO:0000421	SO:0001037	three_prime_terminal_inverted_repeat	SO:0001411
7	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441205	SO:0000422	SO:0001039	U5_LTR_region	SO:0001037
7	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441206	SO:0000423	SO:0001039	R_LTR_region	SO:0001037
7	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441207	SO:0000424	SO:0001039	U3_LTR_region	SO:0001037
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441208	SO:0000425	SO:0001037	five_prime_LTR	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2441209	SO:0000425	SO:0001037	five_prime_LTR	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441210	SO:0000426	SO:0001037	three_prime_LTR	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2441211	SO:0000426	SO:0001037	three_prime_LTR	SO:0001411
7	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441212	SO:0000427	SO:0000101	R_five_prime_LTR_region	SO:0001039
7	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441214	SO:0000428	SO:0000101	U5_five_prime_LTR_region	SO:0001039
7	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441216	SO:0000429	SO:0000101	U3_five_prime_LTR_region	SO:0001039
7	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441218	SO:0000430	SO:0000101	R_three_prime_LTR_region	SO:0001039
7	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441220	SO:0000431	SO:0000101	U3_three_prime_LTR_region	SO:0001039
7	"An MGE that is integrated into the host chromosome." [SO:ke]	\N	integrated_mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441222	SO:0000432	SO:0000101	U5_three_prime_LTR_region	SO:0001039
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A polypurine tract within an LTR_retrotransposon." [SO:ke]	SO	2441227	SO:0000435	SO:0001411	RR_tract	SO:0000001
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"" []	SO	2441228	SO:0000439	SO:0001506	inverted_ring_chromosome	SO:0001026
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	2441232	SO:0000447	SO:0000831	five_prime_UTR_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An intron located in the 5' UTR." [SO:ke]	SO	2806617	SO:0000447	SO:0000001	five_prime_UTR_intron	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	2441234	SO:0000448	SO:0000831	three_prime_UTR_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An intron located in the 3' UTR." [SO:ke]	SO	2806618	SO:0000448	SO:0000001	three_prime_UTR_intron	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]	SO	2441236	SO:0000454	SO:0000001	rasiRNA	SO:0000110
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome duplication involving an insertion from another chromosome." [SO:ke]	SO	2441237	SO:0000457	SO:0001026	interchromosomal_duplication	SO:0001260
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441238	SO:0000458	SO:0000298	D_gene_segment	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441239	SO:0000460	SO:0001411	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000001
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	2441240	SO:0000461	SO:0001506	inversion_derived_bipartite_deficiency	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	2441241	SO:0000465	SO:0001506	inversion_derived_deficiency_plus_duplication	SO:0001026
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441242	SO:0000466	SO:0000298	V_gene_segment	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441243	SO:0000470	SO:0000298	J_gene_segment	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441244	SO:0000478	SO:0000298	C_gene_segment	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441247	SO:0000482	SO:0001411	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441249	SO:0000485	SO:0000298	DJ_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441251	SO:0000487	SO:0000298	VDJ_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441252	SO:0000488	SO:0000298	VDJ_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441253	SO:0000489	SO:0000298	VJ_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441254	SO:0000490	SO:0000298	VJ_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441255	SO:0000491	SO:0000298	VJ_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2441256	SO:0000492	SO:0000298	D_gene_recombination_feature	SO:0001411
8	"" []	\N	recombination_feature	\N	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2625340	SO:0000493	SO:0000669	three_prime_D_heptamer	SO:0000298
8	"" []	\N	recombination_feature	\N	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2625341	SO:0000494	SO:0000669	three_prime_D_nonamer	SO:0000298
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2806619	SO:0000495	SO:0000298	three_prime_D_spacer	SO:0001411
8	"" []	\N	recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2625342	SO:0000496	SO:0000669	five_prime_D_heptamer	SO:0000298
8	"" []	\N	recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2625343	SO:0000497	SO:0000669	five_prime_D_nonamer	SO:0000298
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2806620	SO:0000498	SO:0000298	five_prime_D_spacer	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441263	SO:0000504	SO:0000298	D_DJ_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441264	SO:0000505	SO:0000298	D_DJ_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441265	SO:0000506	SO:0000298	D_DJ_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441266	SO:0000508	SO:0000298	D_DJ_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441267	SO:0000509	SO:0000298	D_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441268	SO:0000510	SO:0000298	VD_gene_segment	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441269	SO:0000511	SO:0000298	J_C_cluster	SO:0001411
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	2441270	SO:0000512	SO:0001506	inversion_derived_deficiency_plus_aneuploid	SO:0001026
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441271	SO:0000513	SO:0000298	J_cluster	SO:0001411
7	"" []	\N	recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441272	SO:0000514	SO:0000669	J_nonamer	SO:0000298
7	"" []	\N	recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441273	SO:0000515	SO:0000669	J_heptamer	SO:0000298
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2625344	SO:0000517	SO:0000298	J_spacer	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441275	SO:0000518	SO:0000298	V_DJ_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441276	SO:0000519	SO:0000298	V_DJ_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441277	SO:0000520	SO:0000298	V_VDJ_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441278	SO:0000521	SO:0000298	V_VDJ_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441279	SO:0000522	SO:0000298	V_VDJ_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441280	SO:0000523	SO:0000298	V_VJ_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441281	SO:0000524	SO:0000298	V_VJ_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441282	SO:0000525	SO:0000298	V_VJ_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441283	SO:0000526	SO:0000298	V_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441284	SO:0000527	SO:0000298	V_D_DJ_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441285	SO:0000528	SO:0000298	V_D_DJ_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441286	SO:0000529	SO:0000298	V_D_DJ_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441287	SO:0000530	SO:0000298	V_D_DJ_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441288	SO:0000531	SO:0000298	V_D_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441289	SO:0000532	SO:0000298	V_D_J_cluster	SO:0001411
7	"" []	\N	recombination_feature	\N	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441290	SO:0000533	SO:0000669	V_heptamer	SO:0000298
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441291	SO:0000534	SO:0000298	V_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441292	SO:0000535	SO:0000298	V_J_C_cluster	SO:0001411
7	"" []	\N	recombination_feature	\N	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441293	SO:0000536	SO:0000669	V_nonamer	SO:0000298
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2625345	SO:0000537	SO:0000298	V_spacer	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441295	SO:0000538	SO:0000298	V_gene_recombination_feature	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441296	SO:0000539	SO:0000298	DJ_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441297	SO:0000540	SO:0000298	DJ_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441298	SO:0000541	SO:0000298	VDJ_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441299	SO:0000542	SO:0000298	V_DJ_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	SO	2441301	SO:0000545	SO:0000831	recoding_pseudoknot	SO:0001411
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	2441302	SO:0000547	SO:0001506	inversion_derived_bipartite_duplication	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	2441303	SO:0000549	SO:0001506	inversion_derived_duplication_plus_aneuploid	SO:0001026
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	2806621	SO:0000552	SO:0000831	Shine_Dalgarno_sequence	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]	SO	3023308	SO:0000552	SO:0000001	Shine_Dalgarno_sequence	SO:0000110
7	"" []	\N	recombination_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441308	SO:0000556	SO:0000669	five_prime_D_recombination_signal_sequence	SO:0000298
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441310	SO:0000558	SO:0000298	C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441311	SO:0000559	SO:0000298	D_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441312	SO:0000560	SO:0000298	D_J_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441313	SO:0000561	SO:0000298	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"" []	SO	2441314	SO:0000562	SO:0000298	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441315	SO:0000563	SO:0001411	vertebrate_immune_system_gene_recombination_spacer	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441316	SO:0000564	SO:0000298	V_DJ_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441317	SO:0000565	SO:0000298	V_VDJ_J_C_cluster	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441318	SO:0000566	SO:0000298	V_VJ_J_C_cluster	SO:0001411
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]	SO	2441319	SO:0000567	SO:0001026	inversion_derived_aneuploid_chromosome	SO:0001260
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441320	SO:0000568	SO:0001411	bidirectional_promoter	SO:0000001
7	"" []	\N	recombination_feature	\N	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441321	SO:0000570	SO:0000669	three_prime_D_recombination_signal_sequence	SO:0000298
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441322	SO:0000572	SO:0000298	DJ_gene_segment	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441323	SO:0000574	SO:0000298	VDJ_gene_segment	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2441324	SO:0000576	SO:0000298	VJ_gene_segment	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	2441325	SO:0000580	SO:0001411	methylation_guide_snoRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	2441326	SO:0000582	SO:0001411	rRNA_cleavage_snoRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	2441327	SO:0000584	SO:0001411	tmRNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]	SO	2441328	SO:0000586	SO:0000001	tmRNA_primary_transcript	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	2441329	SO:0000587	SO:0000831	group_I_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	SO	2806623	SO:0000587	SO:0000001	group_I_intron	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a signal recognition particle RNA." [SO:ke]	SO	2441332	SO:0000589	SO:0000001	SRP_RNA_primary_transcript	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	SO	2441333	SO:0000590	SO:0000001	SRP_RNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	2441334	SO:0000593	SO:0001411	C_D_box_snoRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	2441335	SO:0000594	SO:0001411	H_ACA_box_snoRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	2441336	SO:0000595	SO:0001411	C_D_box_snoRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	2441337	SO:0000596	SO:0001411	H_ACA_box_snoRNA_primary_transcript	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]	SO	2441338	SO:0000602	SO:0000001	guide_RNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	2441339	SO:0000603	SO:0000831	group_II_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	SO	2806624	SO:0000603	SO:0000001	group_II_intron	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]	SO	2806627	SO:0000613	SO:0000001	bacterial_RNApol_promoter	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A terminator signal for RNA polymerase III transcription." [SO:ke]	SO	2625346	SO:0000615	SO:0000001	terminator_of_type_2_RNApol_III_promoter	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2441343	SO:0000617	SO:0005836	RNApol_III_promoter_type_1	SO:0000831
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2441344	SO:0000618	SO:0005836	RNApol_III_promoter_type_2	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	2441345	SO:0000619	SO:0001411	A_box	SO:0000001
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	2995367	SO:0000620	SO:0001411	B_box	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	2441347	SO:0000620	SO:0001679	B_box	SO:0005836
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"" []	SO	2441348	SO:0000621	SO:0005836	RNApol_III_promoter_type_3	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	2995369	SO:0000622	SO:0001411	C_box	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	2441350	SO:0000622	SO:0001679	C_box	SO:0005836
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	2441351	SO:0000625	SO:0001411	silencer	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]	SO	2441352	SO:0000627	SO:0000001	insulator	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	2441353	SO:0000630	SO:0000831	upstream_AUG_codon	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A start codon upstream of the ORF." [SO:ke]	SO	2806629	SO:0000630	SO:0000001	upstream_AUG_codon	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	2625348	SO:0000639	SO:0000831	internal_transcribed_spacer_region	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]	SO	2939578	SO:0000639	SO:0000001	internal_transcribed_spacer_region	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	2625349	SO:0000640	SO:0000831	external_transcribed_spacer_region	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]	SO	2939579	SO:0000640	SO:0000001	external_transcribed_spacer_region	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441360	SO:0000641	SO:0000001	tetranucleotide_repeat_microsatellite_feature	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]	SO	2441361	SO:0000644	SO:0000001	antisense_RNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]	SO	2441362	SO:0000646	SO:0000001	siRNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a micro RNA." [SO:ke]	SO	2441363	SO:0000647	SO:0000001	miRNA_primary_transcript	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	2441364	SO:0000648	SO:0001411	stRNA_primary_transcript	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]	SO	2441365	SO:0000649	SO:0000001	stRNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	2441366	SO:0000650	SO:0001411	small_subunit_rRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	2441367	SO:0000651	SO:0001411	large_subunit_rRNA	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	2441368	SO:0000652	SO:0000831	rRNA_5S	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	2441369	SO:0000653	SO:0000831	rRNA_28S	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	2441372	SO:0000676	SO:0000673	canonical_three_prime_splice_site	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	2885716	SO:0000676	SO:0001411	canonical_three_prime_splice_site	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	2441374	SO:0000677	SO:0000673	canonical_five_prime_splice_site	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	2885717	SO:0000677	SO:0001411	canonical_five_prime_splice_site	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	2441376	SO:0000678	SO:0000673	non_canonical_three_prime_splice_site	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	2885718	SO:0000678	SO:0001411	non_canonical_three_prime_splice_site	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	2441378	SO:0000679	SO:0000673	non_canonical_five_prime_splice_site	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	2885719	SO:0000679	SO:0001411	non_canonical_five_prime_splice_site	SO:0000001
8	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2625350	SO:0000680	SO:0000233	non_canonical_start_codon	SO:0000673
8	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2625351	SO:0000680	SO:0000833	non_canonical_start_codon	SO:0000673
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2625352	SO:0000680	SO:0000833	non_canonical_start_codon	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	2441383	SO:0000683	SO:0001411	exonic_splice_enhancer	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]	SO	2441384	SO:0000684	SO:0000001	nuclease_sensitive_site	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"" []	SO	2441385	SO:0000685	SO:0000409	DNAseI_hypersensitive_site	SO:0001411
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	2441386	SO:0000686	SO:0001506	translocation_element	SO:0001026
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	2441387	SO:0000706	SO:0000831	trans_splice_acceptor_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The 3' splice site of the acceptor primary transcript." [SO:ke]	SO	2806632	SO:0000706	SO:0000001	trans_splice_acceptor_site	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	2441389	SO:0000707	SO:0000831	trans_splice_donor_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The 5' five prime splice site region of the donor RNA." [SO:ke]	SO	2806633	SO:0000707	SO:0000001	trans_splice_donor_site	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	2441391	SO:0000708	SO:0000673	SL1_acceptor_site	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	2885723	SO:0000708	SO:0001411	SL1_acceptor_site	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441393	SO:0000709	SO:0000673	SL2_acceptor_site	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885724	SO:0000709	SO:0001411	SL2_acceptor_site	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]	SO	2441395	SO:0000710	SO:0000001	gene_with_stop_codon_redefined_as_selenocysteine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]	SO	2441396	SO:0000727	SO:0000001	CRM	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]	SO	2441397	SO:0000734	SO:0000001	exemplar_mRNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	2441398	SO:0000766	SO:0001411	pyrrolysyl_tRNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cDNA clone invalidated because it is chimeric." [SO:xp]	SO	2441403	SO:0000810	SO:0000001	chimeric_cDNA_clone	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cDNA clone invalidated by genomic contamination." [SO:xp]	SO	2441404	SO:0000811	SO:0000001	genomically_contaminated_cDNA_clone	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cDNA clone invalidated by polyA priming." [SO:xp]	SO	2441405	SO:0000812	SO:0000001	polyA_primed_cDNA_clone	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cDNA invalidated clone by partial processing." [SO:xp]	SO	2441406	SO:0000813	SO:0000001	partially_processed_cDNA_clone	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441408	SO:0000848	SO:0001037	LTR_component	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2441409	SO:0000848	SO:0001037	LTR_component	SO:0001411
7	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441410	SO:0000849	SO:0001039	three_prime_LTR_component	SO:0001037
7	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2441411	SO:0000850	SO:0001039	five_prime_LTR_component	SO:0001037
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA that is capped." [SO:xp]	SO	2441413	SO:0000862	SO:0000001	capped_mRNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA that is polyadenylated." [SO:xp]	SO	2441414	SO:0000871	SO:0000001	polyadenylated_mRNA	SO:0000110
8	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2625354	SO:0000883	SO:0000233	stop_codon_read_through	SO:0000673
8	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2625355	SO:0000883	SO:0000833	stop_codon_read_through	SO:0000673
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2625356	SO:0000883	SO:0000833	stop_codon_read_through	SO:0001411
8	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2625357	SO:0000884	SO:0000234	stop_codon_redefined_as_pyrrolysine	SO:0000233
8	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2625358	SO:0000884	SO:0000834	stop_codon_redefined_as_pyrrolysine	SO:0000833
8	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2625359	SO:0000885	SO:0000234	stop_codon_redefined_as_selenocysteine	SO:0000233
8	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2625360	SO:0000885	SO:0000834	stop_codon_redefined_as_selenocysteine	SO:0000833
7	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]	SO	2441426	SO:0000894	SO:0000733	silenced_by_DNA_modification	SO:0000400
7	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	2441427	SO:0000895	SO:0000401	silenced_by_DNA_methylation	SO:0000733
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625361	SO:0000912	SO:0000001	asx_turn	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441431	SO:0000932	SO:0000001	pre_edited_mRNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	2441432	SO:0000935	SO:0000831	edited_CDS	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CDS that is edited." [SO:xp]	SO	2806636	SO:0000935	SO:0000001	edited_CDS	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441434	SO:0000936	SO:0001411	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441435	SO:0000938	SO:0001411	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441436	SO:0000939	SO:0001411	vertebrate_immune_system_gene_recombination_signal_feature	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	2441438	SO:0000943	SO:0001411	attB_site	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	2441439	SO:0000944	SO:0001411	attL_site	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	2441440	SO:0000945	SO:0001411	attR_site	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]	SO	2441441	SO:0000946	SO:0000001	integration_excision_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]	SO	2441442	SO:0000947	SO:0000001	resolution_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]	SO	2441443	SO:0000948	SO:0000001	inversion_site	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	2441444	SO:0000949	SO:0001411	dif_site	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]	SO	2441446	SO:0000957	SO:0000001	linear_double_stranded_DNA_chromosome	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]	SO	2441447	SO:0000958	SO:0000001	circular_double_stranded_DNA_chromosome	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]	SO	2441448	SO:0000959	SO:0000001	linear_single_stranded_DNA_chromosome	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	2441449	SO:0000960	SO:0000001	circular_single_stranded_DNA_chromosome	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]	SO	2441450	SO:0000963	SO:0000001	linear_single_stranded_RNA_chromosome	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]	SO	2441451	SO:0000964	SO:0000001	linear_double_stranded_RNA_chromosome	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]	SO	2441452	SO:0000966	SO:0000001	circular_single_stranded_RNA_chromosome	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]	SO	2441453	SO:0000967	SO:0000001	circular_double_stranded_RNA_chromosome	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	2706735	SO:0000973	SO:0000001	insertion_sequence	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]	SO	2441455	SO:0000973	SO:0001411	insertion_sequence	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2625364	SO:0000981	SO:0000001	rho_dependent_bacterial_terminator	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2625365	SO:0000982	SO:0000001	rho_independent_bacterial_terminator	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	2441459	SO:0000989	SO:0000001	class_II_RNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]	SO	2441460	SO:0000990	SO:0000001	class_I_RNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	2441462	SO:0000998	SO:0000831	recursive_splice_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]	SO	2806637	SO:0000998	SO:0000001	recursive_splice_site	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	2441464	SO:0001000	SO:0000831	rRNA_16S	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	2441465	SO:0001001	SO:0000831	rRNA_23S	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	2441466	SO:0001002	SO:0000831	rRNA_25S	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	2441467	SO:0001003	SO:0001037	solo_LTR	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recombination product between the 2 LTR of the same element." [SO:ke]	SO	2441468	SO:0001003	SO:0001037	solo_LTR	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]	SO	2441470	SO:0001035	SO:0000001	piRNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	2441471	SO:0001036	SO:0001411	arginyl_tRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	2441472	SO:0001043	SO:0001411	attCtn_site	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]	SO	2706743	SO:0001043	SO:0000001	attCtn_site	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	2441474	SO:0001046	SO:0001411	IRLinv_site	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	2441475	SO:0001047	SO:0001411	IRRinv_site	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region located within an inversion site." [SO:ke]	SO	2441476	SO:0001048	SO:0000001	inversion_site_part	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]	SO	2441478	SO:0001058	SO:0000001	promoter_targeting_sequence	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]	SO	2625368	SO:0001089	SO:0000001	post_translationally_modified_region	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]	SO	2441481	SO:0001092	SO:0000104	polypeptide_metal_contact	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]	SO	2441483	SO:0001093	SO:0000104	protein_protein_contact	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	2441485	SO:0001094	SO:0000839	polypeptide_calcium_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	2441486	SO:0001094	SO:0000839	polypeptide_calcium_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	2441487	SO:0001095	SO:0000839	polypeptide_cobalt_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	2441488	SO:0001095	SO:0000839	polypeptide_cobalt_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	2441489	SO:0001096	SO:0000839	polypeptide_copper_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	2441490	SO:0001096	SO:0000839	polypeptide_copper_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	2441491	SO:0001097	SO:0000839	polypeptide_iron_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	2441492	SO:0001097	SO:0000839	polypeptide_iron_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	2441493	SO:0001098	SO:0000839	polypeptide_magnesium_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	2441494	SO:0001098	SO:0000839	polypeptide_magnesium_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	2441495	SO:0001099	SO:0000839	polypeptide_manganese_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	2441496	SO:0001099	SO:0000839	polypeptide_manganese_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	2441497	SO:0001100	SO:0000839	polypeptide_molybdenum_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	2441498	SO:0001100	SO:0000839	polypeptide_molybdenum_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	2441499	SO:0001101	SO:0000839	polypeptide_nickel_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	2441500	SO:0001101	SO:0000839	polypeptide_nickel_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	2441501	SO:0001102	SO:0000839	polypeptide_tungsten_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	2441502	SO:0001102	SO:0000839	polypeptide_tungsten_ion_contact_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	2441503	SO:0001103	SO:0000839	polypeptide_zinc_ion_contact_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	2441504	SO:0001103	SO:0000839	polypeptide_zinc_ion_contact_site	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Residues which interact with a ligand." [EBIBS:GAR]	SO	2441507	SO:0001105	SO:0000104	polypeptide_ligand_contact	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625369	SO:0001109	SO:0000001	beta_bulge_loop_five	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625370	SO:0001110	SO:0000001	beta_bulge_loop_six	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	2625371	SO:0001112	SO:0000001	antiparallel_beta_strand	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]	SO	2625372	SO:0001113	SO:0000001	parallel_beta_strand	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]	SO	2625373	SO:0001115	SO:0000001	left_handed_peptide_helix	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]	SO	2625374	SO:0001116	SO:0000001	right_handed_peptide_helix	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	2441521	SO:0001117	SO:0000104	alpha_helix	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	2706769	SO:0001117	SO:0001411	alpha_helix	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	2441523	SO:0001118	SO:0000104	pi_helix	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	2706771	SO:0001118	SO:0001411	pi_helix	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	2441525	SO:0001119	SO:0000104	three_ten_helix	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	2706773	SO:0001119	SO:0001411	three_ten_helix	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625375	SO:0001121	SO:0000001	polypeptide_nest_left_right_motif	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625376	SO:0001122	SO:0000001	polypeptide_nest_right_left_motif	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625377	SO:0001124	SO:0000001	schellmann_loop_seven	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625378	SO:0001125	SO:0000001	schellmann_loop_six	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441535	SO:0001129	SO:0000104	asx_turn_left_handed_type_one	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706775	SO:0001129	SO:0001411	asx_turn_left_handed_type_one	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441537	SO:0001130	SO:0000104	asx_turn_left_handed_type_two	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706777	SO:0001130	SO:0001411	asx_turn_left_handed_type_two	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441539	SO:0001131	SO:0000104	asx_turn_right_handed_type_two	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706779	SO:0001131	SO:0001411	asx_turn_right_handed_type_two	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441541	SO:0001132	SO:0000104	asx_turn_right_handed_type_one	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706781	SO:0001132	SO:0001411	asx_turn_right_handed_type_one	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625379	SO:0001133	SO:0000001	beta_turn	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441545	SO:0001134	SO:0000104	beta_turn_left_handed_type_one	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706783	SO:0001134	SO:0001411	beta_turn_left_handed_type_one	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441547	SO:0001135	SO:0000104	beta_turn_left_handed_type_two	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706785	SO:0001135	SO:0001411	beta_turn_left_handed_type_two	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441549	SO:0001136	SO:0000104	beta_turn_right_handed_type_one	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706787	SO:0001136	SO:0001411	beta_turn_right_handed_type_one	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441551	SO:0001137	SO:0000104	beta_turn_right_handed_type_two	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706789	SO:0001137	SO:0001411	beta_turn_right_handed_type_two	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625380	SO:0001138	SO:0000001	gamma_turn	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441555	SO:0001139	SO:0000104	gamma_turn_classic	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706791	SO:0001139	SO:0001411	gamma_turn_classic	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441557	SO:0001140	SO:0000104	gamma_turn_inverse	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706793	SO:0001140	SO:0001411	gamma_turn_inverse	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2625381	SO:0001141	SO:0000001	serine_threonine_turn	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441561	SO:0001142	SO:0000104	st_turn_left_handed_type_one	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706795	SO:0001142	SO:0001411	st_turn_left_handed_type_one	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441563	SO:0001143	SO:0000104	st_turn_left_handed_type_two	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706797	SO:0001143	SO:0001411	st_turn_left_handed_type_two	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441565	SO:0001144	SO:0000104	st_turn_right_handed_type_one	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706799	SO:0001144	SO:0001411	st_turn_right_handed_type_one	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2441567	SO:0001145	SO:0000104	st_turn_right_handed_type_two	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2706801	SO:0001145	SO:0001411	st_turn_right_handed_type_two	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	2441569	SO:0001150	SO:0000104	beta_turn_type_six	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	2706803	SO:0001150	SO:0001411	beta_turn_type_six	SO:0000001
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2441571	SO:0001151	SO:0000839	beta_turn_type_six_a	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2441572	SO:0001151	SO:0000839	beta_turn_type_six_a	SO:0001411
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"" []	SO	2441573	SO:0001152	SO:0001070	beta_turn_type_six_a_one	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	biosapiens	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"" []	SO	2441574	SO:0001153	SO:0001070	beta_turn_type_six_a_two	SO:0000839
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2441575	SO:0001154	SO:0000839	beta_turn_type_six_b	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2441576	SO:0001154	SO:0000839	beta_turn_type_six_b	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	2441577	SO:0001155	SO:0000104	beta_turn_type_eight	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	2706813	SO:0001155	SO:0001411	beta_turn_type_eight	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	2441579	SO:0001156	SO:0005836	DRE_motif	SO:0000831
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]	SO	2441580	SO:0001157	SO:0000001	DMv4_motif	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	2441581	SO:0001158	SO:0005836	E_box_motif	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2939580	SO:0001159	SO:0000001	DMv5_motif	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2441583	SO:0001159	SO:0005836	DMv5_motif	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	2939581	SO:0001160	SO:0000001	DMv3_motif	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	2441585	SO:0001160	SO:0005836	DMv3_motif	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2939582	SO:0001161	SO:0000001	DMv2_motif	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2441587	SO:0001161	SO:0005836	DMv2_motif	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	2995380	SO:0001162	SO:0001411	MTE	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	2441589	SO:0001162	SO:0001679	MTE	SO:0005836
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	2441590	SO:0001163	SO:0005836	INR1_motif	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	2939583	SO:0001164	SO:0000001	DPE1_motif	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	2441592	SO:0001164	SO:0005836	DPE1_motif	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	2939584	SO:0001165	SO:0000001	DMv1_motif	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	2441594	SO:0001165	SO:0005836	DMv1_motif	SO:0000831
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	2441595	SO:0001166	SO:0005836	GAGA_motif	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	2939585	SO:0001167	SO:0000001	NDM2_motif	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	2441597	SO:0001167	SO:0005836	NDM2_motif	SO:0000831
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	2939586	SO:0001168	SO:0000001	NDM3_motif	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	2441599	SO:0001168	SO:0005836	NDM3_motif	SO:0000831
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	2706828	SO:0001170	SO:0000001	polinton	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]	SO	2441601	SO:0001170	SO:0001411	polinton	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	2441602	SO:0001171	SO:0000831	rRNA_21S	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	2441608	SO:0001178	SO:0001411	pyrrolysine_tRNA_primary_transcript	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	2441609	SO:0001179	SO:0000831	U3_snoRNA	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	2625387	SO:0001180	SO:0000831	AU_rich_element	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]	SO	2939587	SO:0001180	SO:0000001	AU_rich_element	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	2625389	SO:0001181	SO:0000831	Bruno_response_element	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]	SO	2939588	SO:0001181	SO:0000001	Bruno_response_element	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	2441614	SO:0001182	SO:0000831	iron_responsive_element	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]	SO	2806642	SO:0001182	SO:0000001	iron_responsive_element	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	2441616	SO:0001187	SO:0000831	pseudouridylation_guide_snoRNA	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An oligo composed of (R)-GNA residues." [RSC:cb]	SO	2441617	SO:0001195	SO:0000001	R_GNA_oligo	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An oligo composed of (S)-GNA residues." [RSC:cb]	SO	2441618	SO:0001197	SO:0000001	S_GNA_oligo	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2441619	SO:0001203	SO:0001411	RNA_polymerase_promoter	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2441620	SO:0001204	SO:0000831	Phage_RNA_Polymerase_Promoter	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2441621	SO:0001205	SO:0005836	SP6_RNA_Polymerase_Promoter	SO:0000831
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2441622	SO:0001206	SO:0005836	T3_RNA_Polymerase_Promoter	SO:0000831
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2441623	SO:0001207	SO:0005836	T7_RNA_Polymerase_Promoter	SO:0000831
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	2441624	SO:0001208	SO:0000001	five_prime_EST	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	SO	2441625	SO:0001209	SO:0000001	three_prime_EST	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2441627	SO:0001211	SO:0000831	plus_1_translational_frameshift	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2806643	SO:0001211	SO:0000001	plus_1_translational_frameshift	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2441629	SO:0001212	SO:0000831	plus_2_translational_frameshift	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]	SO	2806644	SO:0001212	SO:0000001	plus_2_translational_frameshift	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	2441631	SO:0001213	SO:0000831	group_III_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]	SO	2806645	SO:0001213	SO:0000001	group_III_intron	SO:0000110
7	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]	SO	2441634	SO:0001220	SO:0000733	silenced_by_RNA_interference	SO:0000400
7	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]	SO	2441635	SO:0001221	SO:0000733	silenced_by_histone_modification	SO:0000400
7	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	2441636	SO:0001222	SO:0000401	silenced_by_histone_methylation	SO:0000733
7	"An attribute describing a located_sequence_feature." [SO:ke]	\N	feature_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	2441637	SO:0001223	SO:0000401	silenced_by_histone_deacetylation	SO:0000733
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]	SO	2441638	SO:0001233	SO:0000001	methylinosine	SO:0000110
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]	SO	2441644	SO:0001255	SO:0001026	autopolyploid	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]	SO	2441645	SO:0001256	SO:0001026	allopolyploid	SO:0001260
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]	SO	2441646	SO:0001257	SO:0000001	homing_endonuclease_binding_site	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	2441647	SO:0001258	SO:0005836	octamer_motif	SO:0000831
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	2441648	SO:0001278	SO:0000001	one_methylinosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	2441649	SO:0001279	SO:0000001	one_two_prime_O_dimethylinosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]	SO	2441650	SO:0001280	SO:0000001	two_prime_O_methylinosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2441651	SO:0001317	SO:0000001	queuosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2441652	SO:0001318	SO:0000001	epoxyqueuosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2441653	SO:0001319	SO:0000001	galactosyl_queuosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2441654	SO:0001320	SO:0000001	mannosyl_queuosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2441655	SO:0001321	SO:0000001	seven_cyano_seven_deazaguanosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2441656	SO:0001322	SO:0000001	seven_aminomethyl_seven_deazaguanosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]	SO	2441657	SO:0001323	SO:0000001	archaeosine	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2441658	SO:0001384	SO:0000831	CDS_fragment	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2806646	SO:0001384	SO:0000001	CDS_fragment	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]	SO	2625393	SO:0001422	SO:0000001	conformational_switch	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]	SO	2441665	SO:0001461	SO:0000831	enhancer_binding_site	SO:0001411
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	2441666	SO:0001463	SO:0001411	lincRNA	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]	SO	2441667	SO:0001464	SO:0000001	UST	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	2441668	SO:0001465	SO:0001409	three_prime_UST	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	2441669	SO:0001466	SO:0001409	five_prime_UST	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	2441670	SO:0001467	SO:0000001	RST	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	2441671	SO:0001468	SO:0001409	three_prime_RST	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	2441672	SO:0001469	SO:0001409	five_prime_RST	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2441674	SO:0001482	SO:0000831	shadow_enhancer	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]	SO	2441677	SO:0001493	SO:0001235	centromere_DNA_Element_I	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]	SO	2441679	SO:0001494	SO:0001235	centromere_DNA_Element_II	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]	SO	2441681	SO:0001495	SO:0001235	centromere_DNA_Element_III	SO:0001411
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	2441687	SO:0001567	SO:0001878	stop_retained_variant	SO:0001537
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]	SO	2441688	SO:0001570	SO:0001537	cryptic_splice_acceptor	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]	SO	2441689	SO:0001571	SO:0001537	cryptic_splice_donor	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]	SO	2441690	SO:0001574	SO:0001537	splice_acceptor_variant	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]	SO	2441691	SO:0001575	SO:0001537	splice_donor_variant	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]	SO	2441693	SO:0001582	SO:0001537	initiator_codon_variant	SO:0001060
7	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	2441694	SO:0001583	SO:0001576	missense_variant	SO:0001564
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	2441695	SO:0001585	SO:0001791	conservative_missense_variant	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	2441696	SO:0001585	SO:0001968	conservative_missense_variant	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	2441697	SO:0001586	SO:0001791	non_conservative_missense_variant	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	2441698	SO:0001586	SO:0001968	non_conservative_missense_variant	SO:0001576
7	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	2441699	SO:0001587	SO:0001576	stop_gained	SO:0001564
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	2441700	SO:0001589	SO:0001878	frameshift_variant	SO:0001537
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]	SO	2441701	SO:0001590	SO:0001537	terminator_codon_variant	SO:0001060
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	2441702	SO:0001591	SO:0001564	frame_restoring_variant	SO:0001878
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	2441703	SO:0001592	SO:0001564	minus_1_frameshift_variant	SO:0001878
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"" []	SO	2441704	SO:0001593	SO:0001564	minus_2_frameshift_variant	SO:0001878
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	2441705	SO:0001594	SO:0001564	plus_1_frameshift_variant	SO:0001878
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"" []	SO	2441706	SO:0001595	SO:0001564	plus_2_frameshift_variant	SO:0001878
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]	SO	2441707	SO:0001607	SO:0001537	conservative_amino_acid_substitution	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]	SO	2441708	SO:0001608	SO:0001537	non_conservative_amino_acid_substitution	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	2441709	SO:0001610	SO:0001537	elongated_polypeptide_C_terminal	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	2441710	SO:0001611	SO:0001537	elongated_polypeptide_N_terminal	SO:0001060
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	2441711	SO:0001612	SO:0001878	elongated_in_frame_polypeptide_C_terminal	SO:0001537
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	2441712	SO:0001613	SO:0001878	elongated_out_of_frame_polypeptide_C_terminal	SO:0001537
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	2441713	SO:0001614	SO:0001878	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001537
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	2441714	SO:0001615	SO:0001878	elongated_out_of_frame_polypeptide_N_terminal	SO:0001537
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A UTR variant of the 5' UTR." [SO:ke]	SO	2441715	SO:0001623	SO:0001537	5_prime_UTR_variant	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A UTR variant of the 3' UTR." [SO:ke]	SO	2441716	SO:0001624	SO:0001537	3_prime_UTR_variant	SO:0001060
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	2625394	SO:0001626	SO:0001878	incomplete_terminal_codon_variant	SO:0001537
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	2806651	SO:0001647	SO:0000831	kozak_sequence	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]	SO	3023309	SO:0001647	SO:0000001	kozak_sequence	SO:0000110
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	2441720	SO:0001650	SO:0001878	inframe_variant	SO:0001537
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2441722	SO:0001660	SO:0000001	core_promoter_element	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	2441723	SO:0001661	SO:0001683	RNA_polymerase_II_TATA_box	SO:0001411
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	2441724	SO:0001661	SO:0001679	RNA_polymerase_II_TATA_box	SO:0005836
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	2441725	SO:0001662	SO:0001683	RNA_polymerase_III_TATA_box	SO:0001411
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	2441726	SO:0001662	SO:0005836	RNA_polymerase_III_TATA_box	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	2995388	SO:0001663	SO:0001411	BREd_motif	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	2441728	SO:0001663	SO:0001679	BREd_motif	SO:0005836
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	2995389	SO:0001664	SO:0001411	DCE	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	2441730	SO:0001664	SO:0001679	DCE	SO:0005836
7	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	2441731	SO:0001665	SO:0001055	DCE_SI	SO:0001679
7	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	2441732	SO:0001666	SO:0001055	DCE_SII	SO:0001679
7	"A regulatory region that is involved in the control of the process of transcription." [SO:ke]	\N	transcription_regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	2441733	SO:0001667	SO:0001055	DCE_SIII	SO:0001679
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	2441734	SO:0001668	SO:0001411	proximal_promoter_element	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	2441735	SO:0001669	SO:0005836	RNApol_II_core_promoter	SO:0000831
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2441736	SO:0001670	SO:0001411	distal_promoter_element	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2806653	SO:0001671	SO:0001411	bacterial_RNApol_promoter_sigma_70	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2806654	SO:0001672	SO:0001411	bacterial_RNApol_promoter_sigma54	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2806655	SO:0001673	SO:0000831	minus_12_signal	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]	SO	2806656	SO:0001674	SO:0000831	minus_24_signal	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	2441743	SO:0001675	SO:0001683	A_box_type_1	SO:0001411
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	2441744	SO:0001675	SO:0001679	A_box_type_1	SO:0005836
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	2441745	SO:0001676	SO:0001683	A_box_type_2	SO:0001411
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	2441746	SO:0001676	SO:0001679	A_box_type_2	SO:0005836
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	2995396	SO:0001677	SO:0001411	intermediate_element	SO:0000001
7	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	2441748	SO:0001677	SO:0001679	intermediate_element	SO:0005836
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]	SO	2441749	SO:0001678	SO:0000001	regulatory_promoter_element	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	SO	2441750	SO:0001698	SO:0000001	ASPE_primer	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	SO	2441751	SO:0001699	SO:0000001	dCAPS_primer	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]	SO	2441752	SO:0001700	SO:0000104	histone_modification	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	2441754	SO:0001701	SO:0000839	histone_methylation_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	2441755	SO:0001701	SO:0000839	histone_methylation_site	SO:0001411
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	2441756	SO:0001702	SO:0000839	histone_acetylation_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	2441757	SO:0001702	SO:0000839	histone_acetylation_site	SO:0001411
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441758	SO:0001703	SO:0001067	H3K9_acetylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070272	SO:0001703	SO:0000001	H3K9_acetylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441760	SO:0001704	SO:0001067	H3K14_acetylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070273	SO:0001704	SO:0000001	H3K14_acetylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441762	SO:0001705	SO:0001067	H3K4_monomethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070274	SO:0001705	SO:0000001	H3K4_monomethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441764	SO:0001706	SO:0001067	H3K4_trimethylation	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070275	SO:0001706	SO:0000001	H3K4_trimethylation	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441766	SO:0001707	SO:0001067	H3K9_trimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070276	SO:0001707	SO:0000001	H3K9_trimethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441768	SO:0001708	SO:0001067	H3K27_monomethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070277	SO:0001708	SO:0000001	H3K27_monomethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441770	SO:0001709	SO:0001067	H3K27_trimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070278	SO:0001709	SO:0000001	H3K27_trimethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441772	SO:0001710	SO:0001067	H3K79_monomethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070279	SO:0001710	SO:0000001	H3K79_monomethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441774	SO:0001711	SO:0001067	H3K79_dimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070280	SO:0001711	SO:0000001	H3K79_dimethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441776	SO:0001712	SO:0001067	H3K79_trimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	3070281	SO:0001712	SO:0000001	H3K79_trimethylation_site	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441778	SO:0001713	SO:0100021	H4K20_monomethylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2441779	SO:0001714	SO:0100021	H2BK5_monomethylation_site	SO:0000839
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]	SO	2441780	SO:0001715	SO:0000001	ISRE	SO:0000110
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	2441781	SO:0001716	SO:0000839	histone_ubiqitination_site	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	2441782	SO:0001716	SO:0000839	histone_ubiqitination_site	SO:0001411
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	2441783	SO:0001717	SO:0100021	H2B_ubiquitination_site	SO:0000839
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2441784	SO:0001718	SO:0001067	H3K18_acetylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	3070282	SO:0001718	SO:0000001	H3K18_acetylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2441786	SO:0001719	SO:0001067	H3K23_acylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	3070283	SO:0001719	SO:0000001	H3K23_acylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2441788	SO:0001721	SO:0001067	H3K27_acylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	3070284	SO:0001721	SO:0000001	H3K27_acylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2441790	SO:0001722	SO:0001067	H3K36_monomethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	3070285	SO:0001722	SO:0000001	H3K36_monomethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	2441792	SO:0001723	SO:0001067	H3K36_dimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	3070286	SO:0001723	SO:0000001	H3K36_dimethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	2441794	SO:0001724	SO:0001067	H3K36_trimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	3070287	SO:0001724	SO:0000001	H3K36_trimethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2441796	SO:0001725	SO:0001067	H3K4_dimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	3070288	SO:0001725	SO:0000001	H3K4_dimethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2441798	SO:0001726	SO:0001067	H3K27_dimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	3070289	SO:0001726	SO:0000001	H3K27_dimethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2441800	SO:0001727	SO:0001067	H3K9_monomethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	3070290	SO:0001727	SO:0000001	H3K9_monomethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	2441802	SO:0001728	SO:0001067	H3K9_dimethylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	3070291	SO:0001728	SO:0000001	H3K9_dimethylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2441804	SO:0001729	SO:0001067	H4K16_acylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	3070292	SO:0001729	SO:0000001	H4K16_acylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2441806	SO:0001730	SO:0001067	H4K5_acylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	3070293	SO:0001730	SO:0000001	H4K5_acylation_site	SO:0000110
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	2441808	SO:0001731	SO:0001067	H4K8_acylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	3070294	SO:0001731	SO:0000001	H4K8_acylation_site	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2441810	SO:0001732	SO:0100021	H3K27_methylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2441811	SO:0001733	SO:0100021	H3K36_methylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	2441812	SO:0001734	SO:0100021	H3K4_methylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2441813	SO:0001735	SO:0100021	H3K79_methylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2441814	SO:0001736	SO:0100021	H3K9_methylation_site	SO:0000839
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	2441815	SO:0001737	SO:0000839	histone_acylation_region	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	2441816	SO:0001737	SO:0000839	histone_acylation_region	SO:0001411
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	2441817	SO:0001738	SO:0100021	H4K_acylation_region	SO:0000839
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441818	SO:0001748	SO:0000185	SL3_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441819	SO:0001748	SO:0000833	SL3_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441820	SO:0001748	SO:0000833	SL3_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441821	SO:0001749	SO:0000185	SL4_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441822	SO:0001749	SO:0000833	SL4_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441823	SO:0001749	SO:0000833	SL4_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441824	SO:0001750	SO:0000185	SL5_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441825	SO:0001750	SO:0000833	SL5_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441826	SO:0001750	SO:0000833	SL5_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441827	SO:0001751	SO:0000185	SL6_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441828	SO:0001751	SO:0000833	SL6_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441829	SO:0001751	SO:0000833	SL6_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441830	SO:0001752	SO:0000185	SL7_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441831	SO:0001752	SO:0000833	SL7_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441832	SO:0001752	SO:0000833	SL7_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441833	SO:0001753	SO:0000185	SL8_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441834	SO:0001753	SO:0000833	SL8_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441835	SO:0001753	SO:0000833	SL8_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441836	SO:0001754	SO:0000185	SL9_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441837	SO:0001754	SO:0000833	SL9_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441838	SO:0001754	SO:0000833	SL9_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441839	SO:0001755	SO:0000185	SL10_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441840	SO:0001755	SO:0000833	SL10_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441841	SO:0001755	SO:0000833	SL10_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441842	SO:0001756	SO:0000185	SL11_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441843	SO:0001756	SO:0000833	SL11_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441844	SO:0001756	SO:0000833	SL11_acceptor_site	SO:0001411
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441845	SO:0001757	SO:0000185	SL12_acceptor_site	SO:0000673
7	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441846	SO:0001757	SO:0000833	SL12_acceptor_site	SO:0000673
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2441847	SO:0001757	SO:0000833	SL12_acceptor_site	SO:0001411
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]	SO	2441848	SO:0001787	SO:0001537	splice_donor_5th_base_variant	SO:0001060
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]	SO	2441850	SO:0001788	SO:0001411	U_box	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]	SO	2441853	SO:0001796	SO:0001235	regional_centromere_central_core	SO:0001411
7	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	2441855	SO:0001798	SO:0000340	regional_centromere_inner_repeat_region	SO:0001235
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]	SO	2441857	SO:0001799	SO:0001235	regional_centromere_outer_repeat_region	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]	SO	2441858	SO:0001800	SO:0000001	tasiRNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a tasiRNA." [PMID:16145017]	SO	2441859	SO:0001801	SO:0000001	tasiRNA_primary_transcript	SO:0000110
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	2441860	SO:0001804	SO:0000839	DDB_box	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	2441861	SO:0001804	SO:0000839	DDB_box	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]	SO	2625395	SO:0001805	SO:0000001	destruction_box	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]	SO	2625396	SO:0001807	SO:0000001	KEN_box	SO:0000110
7	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	2441866	SO:0001810	SO:0000839	PIP_box	SO:0000104
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	2441867	SO:0001810	SO:0000839	PIP_box	SO:0001411
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	2441868	SO:0001811	SO:0000104	phosphorylation_site	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	2706977	SO:0001811	SO:0001411	phosphorylation_site	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]	SO	2806658	SO:0001812	SO:0000001	transmembrane_helix	SO:0000110
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]	SO	2441871	SO:0001818	SO:0001537	protein_altering_variant	SO:0001060
7	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]	SO	2441872	SO:0001819	SO:0001537	synonymous_variant	SO:0001060
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	2441873	SO:0001820	SO:0001564	inframe_indel	SO:0001878
7	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	2441874	SO:0001821	SO:0001576	inframe_insertion	SO:0001564
7	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	2441875	SO:0001822	SO:0001576	inframe_deletion	SO:0001564
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	2441876	SO:0001823	SO:0001791	conservative_inframe_insertion	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	2441877	SO:0001823	SO:0001968	conservative_inframe_insertion	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	2441878	SO:0001824	SO:0001791	disruptive_inframe_insertion	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	2441879	SO:0001824	SO:0001968	disruptive_inframe_insertion	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	2441880	SO:0001825	SO:0001791	conservative_inframe_deletion	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	2441881	SO:0001825	SO:0001968	conservative_inframe_deletion	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	2441882	SO:0001826	SO:0001791	disruptive_inframe_deletion	SO:0001576
7	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	2441883	SO:0001826	SO:0001968	disruptive_inframe_deletion	SO:0001576
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	2441884	SO:0001835	SO:0001411	N_region	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	2441885	SO:0001836	SO:0001411	S_region	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]	SO	2441886	SO:0001839	SO:0000001	CSL_response_element	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	2441887	SO:0001840	SO:0001411	GATA_box	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]	SO	2441888	SO:0001842	SO:0000001	AP_1_binding_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]	SO	2441889	SO:0001843	SO:0000001	CRE	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]	SO	2441890	SO:0001844	SO:0000001	CuRE	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]	SO	2441891	SO:0001845	SO:0000001	DRE	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]	SO	2441892	SO:0001846	SO:0000001	FLEX_element	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]	SO	2441893	SO:0001847	SO:0000001	forkhead_motif	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	2441894	SO:0001848	SO:0001411	homol_D_box	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]	SO	2441895	SO:0001849	SO:0000001	homol_E_box	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]	SO	2441896	SO:0001850	SO:0000001	HSE	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	2441897	SO:0001851	SO:0001683	iron_repressed_GATA_element	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]	SO	2441898	SO:0001852	SO:0000001	mating_type_M_box	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]	SO	2441899	SO:0001855	SO:0000001	MCB	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]	SO	2441900	SO:0001856	SO:0000001	CCAAT_motif	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]	SO	2441901	SO:0001857	SO:0000001	Ace2_UAS	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]	SO	2441902	SO:0001858	SO:0000001	TR_box	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]	SO	2441903	SO:0001859	SO:0000001	STREP_motif	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]	SO	2441904	SO:0001861	SO:0000001	sterol_regulatory_element	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	2441905	SO:0001862	SO:0001411	GT_dinucleotide_repeat	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	2441906	SO:0001863	SO:0001411	GTT_trinucleotide_repeat	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]	SO	2441907	SO:0001865	SO:0000001	CDRE_motif	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]	SO	2441909	SO:0001870	SO:0000001	enhancerRNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]	SO	2441910	SO:0001871	SO:0000001	PCB	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]	SO	2625399	SO:0001875	SO:0000001	unassigned_supercontig	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-coding RNA over 200nucleotides in length." [HGNC:mw]	SO	2441912	SO:0001877	SO:0000001	lnc_RNA	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is part of a transposable element." [SO:ke]	SO	2441913	SO:0001896	SO:0000831	transposable_element_CDS	SO:0001411
7	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2441914	SO:0001898	SO:0000340	dg_repeat	SO:0001235
7	"A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]	\N	replicon	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2441916	SO:0001899	SO:0000340	dh_repeat	SO:0001235
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	2441918	SO:0001901	SO:0001411	AACCCT_box	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	2441919	SO:0001903	SO:0001411	intronic_lncRNA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	2441920	SO:0001904	SO:0001411	antisense_lncRNA	SO:0000001
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]	SO	2441921	SO:0001909	SO:0001564	frameshift_elongation	SO:0001878
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]	SO	2441922	SO:0001910	SO:0001564	frameshift_truncation	SO:0001878
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	2806659	SO:0001913	SO:0001411	bacterial_RNApol_promoter_sigma_ecf	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cytosine methylated at the 5 carbon." [SO:rtapella]	SO	2441924	SO:0001918	SO:0000001	5_methylcytosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cytosine methylated at the 4 nitrogen." [SO:rtapella]	SO	2441925	SO:0001919	SO:0000001	4_methylcytosine	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An adenine methylated at the 6 nitrogen." [SO:rtapella]	SO	2441926	SO:0001920	SO:0000001	N6_methyladenine	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A scaffold composed of mitochondrial contigs." [GMOD:ea]	SO	2625400	SO:0001922	SO:0000001	mitochondrial_supercontig	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	2441928	SO:0001923	SO:0001411	TERRA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	2441929	SO:0001924	SO:0001411	ARRET	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	2441930	SO:0001925	SO:0001411	ARIA	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	2441931	SO:0001926	SO:0001411	anti_ARRET	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]	SO	2441932	SO:0001927	SO:0000001	telomeric_transcript	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	2441933	SO:0001935	SO:0100021	H3K20_trimethylation_site	SO:0000839
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	2441934	SO:0001936	SO:0001067	H3K36_acetylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	3070295	SO:0001936	SO:0000001	H3K36_acetylation_site	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	2441936	SO:0001937	SO:0100021	H2BK12_acetylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2441937	SO:0001938	SO:0100021	H2AK5_acetylation_site	SO:0000839
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2441938	SO:0001939	SO:0001067	H4K12_acetylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	3070296	SO:0001939	SO:0000001	H4K12_acetylation_site	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2441940	SO:0001940	SO:0100021	H2BK120_acetylation_site	SO:0000839
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2441941	SO:0001941	SO:0001067	H4K91_acetylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	3070297	SO:0001941	SO:0000001	H4K91_acetylation_site	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2441943	SO:0001942	SO:0100021	H2BK20_acetylation_site	SO:0000839
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2441944	SO:0001943	SO:0001067	H3K4ac_acetylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	3070298	SO:0001943	SO:0000001	H3K4ac_acetylation_site	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2441946	SO:0001944	SO:0100021	H2AK9_acetylation_site	SO:0000839
7	"A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]	\N	polypeptide_conserved_region	biosapiens	biosapiens	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2441947	SO:0001945	SO:0001067	H3K56_acetylation_site	SO:0100021
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	3070299	SO:0001945	SO:0000001	H3K56_acetylation_site	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2441949	SO:0001946	SO:0100021	H2BK15_acetylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	2441950	SO:0001947	SO:0100021	H3R2_monomethylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2441951	SO:0001948	SO:0100021	H3R2_dimethylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	2441952	SO:0001949	SO:0100021	H4R3_dimethylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	2441953	SO:0001950	SO:0100021	H4K4_trimethylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2441954	SO:0001951	SO:0100021	H3K23_dimethylation_site	SO:0000839
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]	SO	2441955	SO:0001952	SO:0000001	promoter_flanking_region	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	2441957	SO:0001959	SO:0001411	TCT_motif	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]	SO	2441958	SO:0001960	SO:0000001	5_hydroxymethylcytosine	SO:0000110
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2441959	SO:0001972	SO:0100021	histone_4_acylation_site	SO:0000839
7	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2441960	SO:0001973	SO:0100021	histone_3_acetylation_site	SO:0000839
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]	SO	2441961	SO:0001974	SO:0000001	CTCF_binding_site	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	2441962	SO:0001980	SO:0001411	G_box	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	2441963	SO:0001981	SO:0001411	L_box	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	2441964	SO:0001982	SO:0001411	I-box	SO:0000001
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	2441965	SO:0001983	SO:0001878	5_prime_UTR_premature_start_codon_variant	SO:0001537
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	2441966	SO:0001988	SO:0001564	5_prime_UTR_premature_start_codon_gain_variant	SO:0001878
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	2441967	SO:0001989	SO:0001564	5_prime_UTR_premature_start_codon_loss_variant	SO:0001878
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	2441968	SO:0001990	SO:0001564	five_prime_UTR_premature_start_codon_location_variant	SO:0001878
7	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	2441969	SO:0001992	SO:0001564	nonsynonymous_variant	SO:0001878
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	2441970	SO:0001993	SO:0000831	extended_cis_splice_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]	SO	2806660	SO:0001993	SO:0000001	extended_cis_splice_site	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]	SO	2441973	SO:0002006	SO:0000001	zinc_repressed_element	SO:0000110
7	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2441974	SO:0002008	SO:0001580	rare_amino_acid_variant	SO:0001791
7	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2441975	SO:0002008	SO:0001580	rare_amino_acid_variant	SO:0001968
7	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2441976	SO:0002009	SO:0001818	selenocysteine_loss	SO:0001580
7	"A sequence variant that changes the coding sequence." [SO:ke]	\N	coding_sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2441977	SO:0002010	SO:0001818	pyrrolysine_loss	SO:0001580
9	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	2806662	SO:0002012	SO:0001878	start_lost	SO:0001537
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	2441979	SO:0002013	SO:0001878	5_prime_UTR_truncation	SO:0001537
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	2441980	SO:0002014	SO:0001878	5_prime_UTR_elongation	SO:0001537
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	2441981	SO:0002015	SO:0001878	3_prime_UTR_truncation	SO:0001537
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	2441982	SO:0002016	SO:0001878	3_prime_UTR_elongation	SO:0001537
7	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	2441983	SO:0002019	SO:0001878	start_retained_variant	SO:0001537
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. priRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]	SO	2441984	SO:0002022	SO:0000001	priRNA	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]	SO	2441985	SO:0002031	SO:0000001	shRNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	2441986	SO:0005837	SO:0001411	U14_snoRNA_primary_transcript	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	2441987	SO:0005841	SO:0000831	methylation_guide_snoRNA	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]	SO	2441988	SO:0005843	SO:0000001	rRNA_cleavage_RNA	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	2441991	SO:0005856	SO:0001411	selenocysteine_tRNA_primary_transcript	SO:0000001
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	2441992	SO:0005857	SO:0001411	selenocysteinyl_tRNA	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A region that is involved a contact with another molecule." [EBIBS:GAR]	SO	2625403	SO:0100002	SO:0000001	molecular_contact_region	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]	SO	2625404	SO:0100018	SO:0000001	polypeptide_binding_motif	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]	SO	2625405	SO:0100019	SO:0000001	polypeptide_catalytic_motif	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]	SO	2441999	SO:0100020	SO:0000104	polypeptide_DNA_contact	SO:0001411
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transition of a cytidine to a thymine." [SO:ke]	SO	2442001	SO:1000011	SO:0000001	C_to_T_transition	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	2442002	SO:1000012	SO:0001059	C_to_T_transition_at_pCpG_site	SO:0000110
7	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	2442003	SO:1000012	SO:0001411	C_to_T_transition_at_pCpG_site	SO:0000001
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2442004	SO:1000013	SO:0000001	T_to_C_transition	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transition of an adenine to a guanine." [SO:ke]	SO	2442005	SO:1000015	SO:0000001	A_to_G_transition	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transition of a guanine to an adenine." [SO:ke]	SO	2442006	SO:1000016	SO:0000001	G_to_A_transition	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from cytidine to adenine." [SO:ke]	SO	2442007	SO:1000019	SO:0000001	C_to_A_transversion	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2442008	SO:1000020	SO:0000001	C_to_G_transversion	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from T to A." [SO:ke]	SO	2442009	SO:1000021	SO:0000001	T_to_A_transversion	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from T to G." [SO:ke]	SO	2442010	SO:1000022	SO:0000001	T_to_G_transversion	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from adenine to cytidine." [SO:ke]	SO	2442011	SO:1000024	SO:0000001	A_to_C_transversion	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from adenine to thymine." [SO:ke]	SO	2442012	SO:1000025	SO:0000001	A_to_T_transversion	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from guanine to cytidine." [SO:ke]	SO	2442013	SO:1000026	SO:0000001	G_to_C_transversion	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A transversion from guanine to thymine." [SO:ke]	SO	2442014	SO:1000027	SO:0000001	G_to_T_transversion	SO:0000110
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An incomplete chromosome." [SO:ke]	SO	2442015	SO:1000029	SO:0001026	chromosomal_deletion	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]	SO	2442016	SO:1000030	SO:0001026	chromosomal_inversion	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A duplication that occurred within a chromosome." [SO:ke]	SO	2442017	SO:1000038	SO:0001026	intrachromosomal_duplication	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]	SO	2625406	SO:1000041	SO:0001026	intrachromosomal_transposition	SO:0001260
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	2442019	SO:1000043	SO:0001506	Robertsonian_fusion	SO:0001026
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]	SO	2442020	SO:1000044	SO:0001026	chromosomal_translocation	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]	SO	2442021	SO:1000045	SO:0001026	ring_chromosome	SO:0001260
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	2442022	SO:1000046	SO:0001506	pericentric_inversion	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	2442023	SO:1000047	SO:0001506	paracentric_inversion	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	2442024	SO:1000048	SO:0001506	reciprocal_chromosomal_translocation	SO:0001026
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]	SO	2442025	SO:1000138	SO:0001026	homo_compound_chromosome	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]	SO	2442026	SO:1000140	SO:0001026	hetero_compound_chromosome	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome that occurred by the division of a larger chromosome." [SO:ke]	SO	2442027	SO:1000141	SO:0001026	chromosome_fission	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]	SO	2442028	SO:1000142	SO:0001026	dexstrosynaptic_chromosome	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]	SO	2442029	SO:1000143	SO:0001026	laevosynaptic_chromosome	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]	SO	2442030	SO:1000144	SO:0001026	free_duplication	SO:0001260
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	2442031	SO:1000145	SO:0001506	free_ring_duplication	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	2442032	SO:1000147	SO:0001506	deficient_translocation	SO:0001026
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]	SO	2625407	SO:1000148	SO:0001026	inversion_cum_translocation	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]	SO	2625408	SO:1000149	SO:0001026	bipartite_duplication	SO:0001260
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	2442035	SO:1000150	SO:0001506	cyclic_translocation	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	2442036	SO:1000151	SO:0001506	bipartite_inversion	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2442037	SO:1000152	SO:0001506	uninverted_insertional_duplication	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	2442038	SO:1000153	SO:0001506	inverted_insertional_duplication	SO:0001026
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]	SO	2442039	SO:1000154	SO:0001026	insertional_duplication	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]	SO	2442040	SO:1000155	SO:0001026	interchromosomal_transposition	SO:0001260
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	2442041	SO:1000156	SO:0001506	inverted_interchromosomal_transposition	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2442042	SO:1000157	SO:0001506	uninverted_interchromosomal_transposition	SO:0001026
8	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	2625409	SO:1000158	SO:0001506	inverted_intrachromosomal_transposition	SO:0001026
8	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2625410	SO:1000159	SO:0001506	uninverted_intrachromosomal_transposition	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2442045	SO:1000160	SO:0001506	unoriented_insertional_duplication	SO:0001026
7	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2442046	SO:1000161	SO:0001506	unoriented_interchromosomal_transposition	SO:0001026
8	"A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]	\N	genome	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2625411	SO:1000162	SO:0001506	unoriented_intrachromosomal_transposition	SO:0001026
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]	SO	2625412	SO:1000171	SO:0001026	deficient_inversion	SO:0001260
7	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	2442049	SO:1000175	SO:0001026	partially_characterised_chromosomal_mutation	SO:0001260
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	2442050	SO:1001246	SO:0000831	CDS_independently_known	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CDS with the evidence status of being independently known." [SO:xp]	SO	2806663	SO:1001246	SO:0000001	CDS_independently_known	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	2442052	SO:1001247	SO:0000673	orphan_CDS	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	2885950	SO:1001247	SO:0001411	orphan_CDS	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	2625413	SO:1001249	SO:0000673	CDS_supported_by_domain_match_data	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	2981301	SO:1001249	SO:0001411	CDS_supported_by_domain_match_data	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	2625415	SO:1001251	SO:0000831	CDS_supported_by_sequence_similarity_data	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CDS that is supported by sequence similarity data." [SO:xp]	SO	2939589	SO:1001251	SO:0000001	CDS_supported_by_sequence_similarity_data	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	2442058	SO:1001254	SO:0000831	CDS_predicted	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CDS that is predicted." [SO:ke]	SO	2806665	SO:1001254	SO:0000001	CDS_predicted	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	2625417	SO:1001259	SO:0000673	CDS_supported_by_EST_or_cDNA_data	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	2981302	SO:1001259	SO:0001411	CDS_supported_by_EST_or_cDNA_data	SO:0000001
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	2939590	SO:1001260	SO:0000831	internal_Shine_Dalgarno_sequence	SO:0001411
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]	SO	3070300	SO:1001260	SO:0000001	internal_Shine_Dalgarno_sequence	SO:0000110
7	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	2442064	SO:1001261	SO:0000001	recoded_mRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]	SO	2625421	SO:1001264	SO:0000001	mRNA_recoded_by_translational_bypass	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]	SO	2625422	SO:1001265	SO:0000001	mRNA_recoded_by_codon_redefinition	SO:0000110
8	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2625423	SO:1001269	SO:0000234	four_bp_start_codon	SO:0000233
8	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2625424	SO:1001269	SO:0000834	four_bp_start_codon	SO:0000833
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	2442072	SO:1001271	SO:0000831	archaeal_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]	SO	2806667	SO:1001271	SO:0000001	archaeal_intron	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	2442074	SO:1001272	SO:0000831	tRNA_intron	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]	SO	2806668	SO:1001272	SO:0000001	tRNA_intron	SO:0000110
8	"A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]	\N	mature_transcript	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2625425	SO:1001273	SO:0000234	CTG_start_codon	SO:0000233
8	"A region of a transcript." [SO:ke]	\N	transcript_region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2625426	SO:1001273	SO:0000834	CTG_start_codon	SO:0000833
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	2442080	SO:1001274	SO:0000831	SECIS_element	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]	SO	2806669	SO:1001274	SO:0000001	SECIS_element	SO:0000110
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	2442082	SO:1001277	SO:0000831	three_prime_recoding_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The recoding stimulatory signal located downstream of the recoding site." [SO:ke]	SO	2806670	SO:1001277	SO:0000001	three_prime_recoding_site	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	2442084	SO:1001279	SO:0000673	three_prime_stem_loop_structure	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	2885957	SO:1001279	SO:0001411	three_prime_stem_loop_structure	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	2442086	SO:1001280	SO:0000831	five_prime_recoding_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The recoding stimulatory signal located upstream of the recoding site." [SO:ke]	SO	2806671	SO:1001280	SO:0000001	five_prime_recoding_site	SO:0000110
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	2442088	SO:1001281	SO:0000673	flanking_three_prime_quadruplet_recoding_signal	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	2885958	SO:1001281	SO:0001411	flanking_three_prime_quadruplet_recoding_signal	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	2442090	SO:1001282	SO:0000673	UAG_stop_codon_signal	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	2885959	SO:1001282	SO:0001411	UAG_stop_codon_signal	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	2442092	SO:1001283	SO:0000673	UAA_stop_codon_signal	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	2885960	SO:1001283	SO:0001411	UAA_stop_codon_signal	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	2442094	SO:1001285	SO:0000673	UGA_stop_codon_signal	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	2885961	SO:1001285	SO:0001411	UGA_stop_codon_signal	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	2442096	SO:1001286	SO:0000673	three_prime_repeat_recoding_signal	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	2885962	SO:1001286	SO:0001411	three_prime_repeat_recoding_signal	SO:0000001
7	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	2442098	SO:1001287	SO:0000673	distant_three_prime_recoding_signal	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	2885963	SO:1001287	SO:0001411	distant_three_prime_recoding_signal	SO:0000001
7	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	2442100	SO:1001288	SO:0000831	stop_codon_signal	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]	SO	2806672	SO:1001288	SO:0000001	stop_codon_signal	SO:0000110
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	3034760	SO:0000014	SO:0000001	INR_motif	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	2706450	SO:0000014	SO:0005836	INR_motif	SO:0000831
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	3034761	SO:0000015	SO:0000001	DPE_motif	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	2706452	SO:0000015	SO:0005836	DPE_motif	SO:0000831
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	3034762	SO:0000016	SO:0000001	BREu_motif	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	2706454	SO:0000016	SO:0005836	BREu_motif	SO:0000831
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]	SO	2706455	SO:0000023	SO:0000001	K_turn_RNA_motif	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	SO	2706456	SO:0000024	SO:0000001	sarcin_like_RNA_motif	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]	SO	2706457	SO:0000037	SO:0000001	locus_control_region	SO:0000110
9	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	2848874	SO:0000062	SO:0001026	deficient_intrachromosomal_transposition	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]	SO	2706459	SO:0000063	SO:0001026	deficient_interchromosomal_transposition	SO:0001260
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	2848875	SO:0000145	SO:0000831	recoded_codon	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]	SO	3034763	SO:0000145	SO:0000001	recoded_codon	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2706464	SO:0000165	SO:0000001	enhancer	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An enhancer bound by a factor." [SO:xp]	SO	2706465	SO:0000166	SO:0001411	enhancer_bound_by_factor	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	2706466	SO:0000169	SO:0001411	RNApol_I_promoter	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	2706467	SO:0000170	SO:0001411	RNApol_II_promoter	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	2706468	SO:0000171	SO:0001411	RNApol_III_promoter	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2706469	SO:0000172	SO:0000831	CAAT_signal	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]	SO	2706470	SO:0000173	SO:0000831	GC_rich_promoter_region	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]	SO	2706471	SO:0000174	SO:0000001	TATA_box	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding alanyl tRNA." [SO:ke]	SO	2706479	SO:0000211	SO:0000001	alanine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]	SO	2706480	SO:0000212	SO:0000001	arginine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]	SO	2706481	SO:0000213	SO:0000001	asparagine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]	SO	2706482	SO:0000214	SO:0000001	aspartic_acid_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]	SO	2706483	SO:0000215	SO:0000001	cysteine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]	SO	2706484	SO:0000216	SO:0000001	glutamic_acid_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]	SO	2706485	SO:0000217	SO:0000001	glutamine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]	SO	2706486	SO:0000218	SO:0000001	glycine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]	SO	2706487	SO:0000219	SO:0000001	histidine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]	SO	2706488	SO:0000220	SO:0000001	isoleucine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]	SO	2706489	SO:0000221	SO:0000001	leucine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]	SO	2706490	SO:0000222	SO:0000001	lysine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]	SO	2706491	SO:0000223	SO:0000001	methionine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]	SO	2706492	SO:0000224	SO:0000001	phenylalanine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]	SO	2706493	SO:0000225	SO:0000001	proline_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	2706494	SO:0000226	SO:0000001	serine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]	SO	2706495	SO:0000227	SO:0000001	threonine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]	SO	2706496	SO:0000228	SO:0000001	tryptophan_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]	SO	2706497	SO:0000229	SO:0000001	tyrosine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]	SO	2706498	SO:0000230	SO:0000001	valine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]	SO	2706501	SO:0000254	SO:0000001	alanyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]	SO	2706502	SO:0000255	SO:0000001	rRNA_small_subunit_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]	SO	2706503	SO:0000256	SO:0000001	asparaginyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]	SO	2706504	SO:0000257	SO:0000001	aspartyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]	SO	2706505	SO:0000258	SO:0000001	cysteinyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]	SO	2706506	SO:0000259	SO:0000001	glutaminyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]	SO	2706507	SO:0000260	SO:0000001	glutamyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]	SO	2706508	SO:0000261	SO:0000001	glycyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]	SO	2706509	SO:0000262	SO:0000001	histidyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]	SO	2706510	SO:0000263	SO:0000001	isoleucyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]	SO	2706511	SO:0000264	SO:0000001	leucyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]	SO	2706512	SO:0000265	SO:0000001	lysyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]	SO	2706513	SO:0000266	SO:0000001	methionyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]	SO	2706514	SO:0000267	SO:0000001	phenylalanyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]	SO	2706515	SO:0000268	SO:0000001	prolyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]	SO	2706516	SO:0000269	SO:0000001	seryl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]	SO	2706517	SO:0000270	SO:0000001	threonyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]	SO	2706518	SO:0000271	SO:0000001	tryptophanyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]	SO	2706519	SO:0000272	SO:0000001	tyrosyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]	SO	2706520	SO:0000273	SO:0000001	valyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]	SO	2706521	SO:0000276	SO:0000001	miRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA with a minus 1 frameshift." [SO:xp]	SO	2706522	SO:0000282	SO:0000001	mRNA_with_minus_1_frameshift	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706524	SO:0000302	SO:0001411	J_gene_recombination_feature	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	2848877	SO:0000318	SO:0000831	start_codon	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"First codon to be translated by a ribosome." [SO:ke]	SO	3034764	SO:0000318	SO:0000001	start_codon	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	SOFA	biological_region	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	2848879	SO:0000319	SO:0000831	stop_codon	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]	SO	3034765	SO:0000319	SO:0000001	stop_codon	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA with a plus 1 frameshift." [SO:ke]	SO	2706529	SO:0000321	SO:0000001	mRNA_with_plus_1_frameshift	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706530	SO:0000322	SO:0000001	nuclease_hypersensitive_site	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]	SO	2706532	SO:0000325	SO:0000001	rRNA_large_subunit_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An mRNA with a plus 2 frameshift." [SO:xp]	SO	2706534	SO:0000329	SO:0000001	mRNA_with_plus_2_frameshift	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A mRNA with a minus 2 frameshift." [SO:ke]	SO	2706535	SO:0000335	SO:0000001	mRNA_with_minus_2_frameshift	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706537	SO:0000346	SO:0000001	loxP_site	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]	SO	2706538	SO:0000350	SO:0000001	FRT_site	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]	SO	2706539	SO:0000354	SO:0000001	group_1_intron_homing_endonuclease_target_region	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	2706541	SO:0000375	SO:0001411	rRNA_5_8S	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	SO	2706542	SO:0000376	SO:0000001	RNA_6S	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	SO	2706543	SO:0000377	SO:0000001	CsrB_RsmB_RNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	SO	2706544	SO:0000378	SO:0000001	DsrA_RNA	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	2706545	SO:0000379	SO:0001411	GcvB_RNA	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706546	SO:0000381	SO:0000831	group_IIA_intron	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2961206	SO:0000381	SO:0000001	group_IIA_intron	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706548	SO:0000382	SO:0000831	group_IIB_intron	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2961207	SO:0000382	SO:0000001	group_IIB_intron	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	SO	2706550	SO:0000383	SO:0000001	MicF_RNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	SO	2706551	SO:0000384	SO:0000001	OxyS_RNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	SO	2706552	SO:0000387	SO:0000001	RprA_RNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	SO	2706553	SO:0000388	SO:0000001	RRE_RNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	SO	2706554	SO:0000389	SO:0000001	spot_42_RNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	SO	2706555	SO:0000391	SO:0000001	U1_snRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	SO	2706556	SO:0000392	SO:0000001	U2_snRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	2706557	SO:0000393	SO:0000001	U4_snRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]	SO	2706558	SO:0000394	SO:0000001	U4atac_snRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	SO	2706559	SO:0000395	SO:0000001	U5_snRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	SO	2706560	SO:0000396	SO:0000001	U6_snRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	SO	2706561	SO:0000397	SO:0000001	U6atac_snRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]	SO	2706562	SO:0000398	SO:0000001	U11_snRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	SO	2706563	SO:0000399	SO:0000001	U12_snRNA	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	2706564	SO:0000403	SO:0001411	U14_snoRNA	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	2706565	SO:0000407	SO:0001411	rRNA_18S	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706570	SO:0000422	SO:0001037	U5_LTR_region	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706571	SO:0000422	SO:0001037	U5_LTR_region	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706572	SO:0000423	SO:0001037	R_LTR_region	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706573	SO:0000423	SO:0001037	R_LTR_region	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706574	SO:0000424	SO:0001037	U3_LTR_region	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706575	SO:0000424	SO:0001037	U3_LTR_region	SO:0001411
8	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2706580	SO:0000427	SO:0001039	R_five_prime_LTR_region	SO:0001037
8	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2706581	SO:0000428	SO:0001039	U5_five_prime_LTR_region	SO:0001037
8	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2706582	SO:0000429	SO:0001039	U3_five_prime_LTR_region	SO:0001037
8	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2706583	SO:0000430	SO:0001039	R_three_prime_LTR_region	SO:0001037
8	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2706584	SO:0000431	SO:0001039	U3_three_prime_LTR_region	SO:0001037
8	"A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]	\N	mobile_genetic_element	SOFA	SOFA	sequence	"" []	SO	2706585	SO:0000432	SO:0001039	U5_three_prime_LTR_region	SO:0001037
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"" []	SO	2706587	SO:0000439	SO:0001026	inverted_ring_chromosome	SO:0001260
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706590	SO:0000458	SO:0001411	D_gene_segment	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706591	SO:0000460	SO:0000001	vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000110
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]	SO	2706592	SO:0000461	SO:0001026	inversion_derived_bipartite_deficiency	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]	SO	2706593	SO:0000465	SO:0001026	inversion_derived_deficiency_plus_duplication	SO:0001260
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706594	SO:0000466	SO:0001411	V_gene_segment	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706595	SO:0000470	SO:0001411	J_gene_segment	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706596	SO:0000478	SO:0001411	C_gene_segment	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706597	SO:0000482	SO:0000001	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706598	SO:0000485	SO:0001411	DJ_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706599	SO:0000487	SO:0001411	VDJ_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706600	SO:0000488	SO:0001411	VDJ_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706601	SO:0000489	SO:0001411	VJ_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706602	SO:0000490	SO:0001411	VJ_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706603	SO:0000491	SO:0001411	VJ_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706604	SO:0000492	SO:0001411	D_gene_recombination_feature	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2848884	SO:0000493	SO:0000298	three_prime_D_heptamer	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2848885	SO:0000494	SO:0000298	three_prime_D_nonamer	SO:0001411
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2961208	SO:0000495	SO:0001411	three_prime_D_spacer	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2848886	SO:0000496	SO:0000298	five_prime_D_heptamer	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2848887	SO:0000497	SO:0000298	five_prime_D_nonamer	SO:0001411
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2961209	SO:0000498	SO:0001411	five_prime_D_spacer	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706611	SO:0000504	SO:0001411	D_DJ_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706612	SO:0000505	SO:0001411	D_DJ_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706613	SO:0000506	SO:0001411	D_DJ_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706614	SO:0000508	SO:0001411	D_DJ_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706615	SO:0000509	SO:0001411	D_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706616	SO:0000510	SO:0001411	VD_gene_segment	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706617	SO:0000511	SO:0001411	J_C_cluster	SO:0000001
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	2706618	SO:0000512	SO:0001026	inversion_derived_deficiency_plus_aneuploid	SO:0001260
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706619	SO:0000513	SO:0001411	J_cluster	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706620	SO:0000514	SO:0000298	J_nonamer	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706621	SO:0000515	SO:0000298	J_heptamer	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2848888	SO:0000517	SO:0001411	J_spacer	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706623	SO:0000518	SO:0001411	V_DJ_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706624	SO:0000519	SO:0001411	V_DJ_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706625	SO:0000520	SO:0001411	V_VDJ_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706626	SO:0000521	SO:0001411	V_VDJ_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706627	SO:0000522	SO:0001411	V_VDJ_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706628	SO:0000523	SO:0001411	V_VJ_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706629	SO:0000524	SO:0001411	V_VJ_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706630	SO:0000525	SO:0001411	V_VJ_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706631	SO:0000526	SO:0001411	V_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706632	SO:0000527	SO:0001411	V_D_DJ_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706633	SO:0000528	SO:0001411	V_D_DJ_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706634	SO:0000529	SO:0001411	V_D_DJ_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706635	SO:0000530	SO:0001411	V_D_DJ_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706636	SO:0000531	SO:0001411	V_D_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706637	SO:0000532	SO:0001411	V_D_J_cluster	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706638	SO:0000533	SO:0000298	V_heptamer	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706639	SO:0000534	SO:0001411	V_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706640	SO:0000535	SO:0001411	V_J_C_cluster	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706641	SO:0000536	SO:0000298	V_nonamer	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2848889	SO:0000537	SO:0001411	V_spacer	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706643	SO:0000538	SO:0001411	V_gene_recombination_feature	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706644	SO:0000539	SO:0001411	DJ_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706645	SO:0000540	SO:0001411	DJ_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706646	SO:0000541	SO:0001411	VDJ_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706647	SO:0000542	SO:0001411	V_DJ_C_cluster	SO:0000001
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]	SO	2706649	SO:0000547	SO:0001026	inversion_derived_bipartite_duplication	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]	SO	2706650	SO:0000549	SO:0001026	inversion_derived_duplication_plus_aneuploid	SO:0001260
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706651	SO:0000556	SO:0000298	five_prime_D_recombination_signal_sequence	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706652	SO:0000558	SO:0001411	C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706653	SO:0000559	SO:0001411	D_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706654	SO:0000560	SO:0001411	D_J_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706655	SO:0000561	SO:0001411	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706656	SO:0000562	SO:0001411	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706657	SO:0000563	SO:0000001	vertebrate_immune_system_gene_recombination_spacer	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706658	SO:0000564	SO:0001411	V_DJ_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706659	SO:0000565	SO:0001411	V_VDJ_J_C_cluster	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706660	SO:0000566	SO:0001411	V_VJ_J_C_cluster	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706661	SO:0000568	SO:0000001	bidirectional_promoter	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	\N	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706662	SO:0000570	SO:0000298	three_prime_D_recombination_signal_sequence	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706663	SO:0000572	SO:0001411	DJ_gene_segment	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706664	SO:0000574	SO:0001411	VDJ_gene_segment	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2706665	SO:0000576	SO:0001411	VJ_gene_segment	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]	SO	2706666	SO:0000580	SO:0000001	methylation_guide_snoRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]	SO	2706667	SO:0000582	SO:0000001	rRNA_cleavage_snoRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	SO	2706668	SO:0000584	SO:0000001	tmRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	2706670	SO:0000593	SO:0000001	C_D_box_snoRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	SO	2706671	SO:0000594	SO:0000001	H_ACA_box_snoRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]	SO	2706672	SO:0000595	SO:0000001	C_D_box_snoRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]	SO	2706673	SO:0000596	SO:0000001	H_ACA_box_snoRNA_primary_transcript	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706675	SO:0000617	SO:0000831	RNApol_III_promoter_type_1	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706676	SO:0000618	SO:0000831	RNApol_III_promoter_type_2	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]	SO	2706677	SO:0000619	SO:0000001	A_box	SO:0000110
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	3034766	SO:0000620	SO:0000001	B_box	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	2706679	SO:0000620	SO:0005836	B_box	SO:0000831
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706680	SO:0000621	SO:0000831	RNApol_III_promoter_type_3	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	3034767	SO:0000622	SO:0000001	C_box	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	2706682	SO:0000622	SO:0005836	C_box	SO:0000831
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]	SO	2706683	SO:0000625	SO:0000001	silencer	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]	SO	2706687	SO:0000648	SO:0000001	stRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]	SO	2706688	SO:0000650	SO:0000001	small_subunit_rRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]	SO	2706689	SO:0000651	SO:0000001	large_subunit_rRNA	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	2706690	SO:0000652	SO:0001411	rRNA_5S	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	2706691	SO:0000653	SO:0001411	rRNA_28S	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	2706692	SO:0000676	SO:0000831	canonical_three_prime_splice_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke]	SO	2961211	SO:0000676	SO:0000001	canonical_three_prime_splice_site	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	2706694	SO:0000677	SO:0000831	canonical_five_prime_splice_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke]	SO	2961212	SO:0000677	SO:0000001	canonical_five_prime_splice_site	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	2706696	SO:0000678	SO:0000831	non_canonical_three_prime_splice_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke]	SO	2961213	SO:0000678	SO:0000001	non_canonical_three_prime_splice_site	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	2706698	SO:0000679	SO:0000831	non_canonical_five_prime_splice_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke]	SO	2961214	SO:0000679	SO:0000001	non_canonical_five_prime_splice_site	SO:0000110
9	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2848892	SO:0000680	SO:0000673	non_canonical_start_codon	SO:0000831
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	3052364	SO:0000680	SO:0001411	non_canonical_start_codon	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	SO	2706702	SO:0000683	SO:0000001	exonic_splice_enhancer	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706703	SO:0000685	SO:0001411	DNAseI_hypersensitive_site	SO:0000001
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]	SO	2706704	SO:0000686	SO:0001026	translocation_element	SO:0001260
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	2706707	SO:0000708	SO:0000831	SL1_acceptor_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]	SO	2961215	SO:0000708	SO:0000001	SL1_acceptor_site	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706709	SO:0000709	SO:0000831	SL2_acceptor_site	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2961216	SO:0000709	SO:0000001	SL2_acceptor_site	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]	SO	2706711	SO:0000766	SO:0000001	pyrrolysyl_tRNA	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706714	SO:0000849	SO:0001037	three_prime_LTR_component	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706715	SO:0000849	SO:0001037	three_prime_LTR_component	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706716	SO:0000850	SO:0001037	five_prime_LTR_component	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2706717	SO:0000850	SO:0001037	five_prime_LTR_component	SO:0001411
9	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2848894	SO:0000883	SO:0000673	stop_codon_read_through	SO:0000831
11	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	3052365	SO:0000883	SO:0001411	stop_codon_read_through	SO:0000001
9	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2848896	SO:0000884	SO:0000233	stop_codon_redefined_as_pyrrolysine	SO:0000673
9	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2848897	SO:0000884	SO:0000833	stop_codon_redefined_as_pyrrolysine	SO:0000673
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2848898	SO:0000884	SO:0000833	stop_codon_redefined_as_pyrrolysine	SO:0001411
9	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2848899	SO:0000885	SO:0000233	stop_codon_redefined_as_selenocysteine	SO:0000673
9	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2848900	SO:0000885	SO:0000833	stop_codon_redefined_as_selenocysteine	SO:0000673
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2848901	SO:0000885	SO:0000833	stop_codon_redefined_as_selenocysteine	SO:0001411
8	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]	SO	2706726	SO:0000895	SO:0000733	silenced_by_DNA_methylation	SO:0000400
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706728	SO:0000936	SO:0000001	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706729	SO:0000938	SO:0000001	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706730	SO:0000939	SO:0000001	vertebrate_immune_system_gene_recombination_signal_feature	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]	SO	2706731	SO:0000943	SO:0000001	attB_site	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]	SO	2706732	SO:0000944	SO:0000001	attL_site	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]	SO	2706733	SO:0000945	SO:0000001	attR_site	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]	SO	2706734	SO:0000949	SO:0000001	dif_site	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	2706737	SO:0001000	SO:0001411	rRNA_16S	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	2706738	SO:0001001	SO:0001411	rRNA_23S	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	SOFA	region	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	2706739	SO:0001002	SO:0001411	rRNA_25S	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]	SO	2706742	SO:0001036	SO:0000001	arginyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]	SO	2706744	SO:0001046	SO:0000001	IRLinv_site	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]	SO	2706745	SO:0001047	SO:0000001	IRRinv_site	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]	SO	2706748	SO:0001094	SO:0000104	polypeptide_calcium_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]	SO	2706750	SO:0001095	SO:0000104	polypeptide_cobalt_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]	SO	2706752	SO:0001096	SO:0000104	polypeptide_copper_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]	SO	2706754	SO:0001097	SO:0000104	polypeptide_iron_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]	SO	2706756	SO:0001098	SO:0000104	polypeptide_magnesium_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]	SO	2706758	SO:0001099	SO:0000104	polypeptide_manganese_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]	SO	2706760	SO:0001100	SO:0000104	polypeptide_molybdenum_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]	SO	2706762	SO:0001101	SO:0000104	polypeptide_nickel_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]	SO	2706764	SO:0001102	SO:0000104	polypeptide_tungsten_ion_contact_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]	SO	2706766	SO:0001103	SO:0000104	polypeptide_zinc_ion_contact_site	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]	SO	2848902	SO:0001117	SO:0000001	alpha_helix	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]	SO	2848903	SO:0001118	SO:0000001	pi_helix	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]	SO	2848904	SO:0001119	SO:0000001	three_ten_helix	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848905	SO:0001129	SO:0000001	asx_turn_left_handed_type_one	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848906	SO:0001130	SO:0000001	asx_turn_left_handed_type_two	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848907	SO:0001131	SO:0000001	asx_turn_right_handed_type_two	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848908	SO:0001132	SO:0000001	asx_turn_right_handed_type_one	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848909	SO:0001134	SO:0000001	beta_turn_left_handed_type_one	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848910	SO:0001135	SO:0000001	beta_turn_left_handed_type_two	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848911	SO:0001136	SO:0000001	beta_turn_right_handed_type_one	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848912	SO:0001137	SO:0000001	beta_turn_right_handed_type_two	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848913	SO:0001139	SO:0000001	gamma_turn_classic	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848914	SO:0001140	SO:0000001	gamma_turn_inverse	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848915	SO:0001142	SO:0000001	st_turn_left_handed_type_one	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848916	SO:0001143	SO:0000001	st_turn_left_handed_type_two	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848917	SO:0001144	SO:0000001	st_turn_right_handed_type_one	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	SO	2848918	SO:0001145	SO:0000001	st_turn_right_handed_type_two	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]	SO	2848919	SO:0001150	SO:0000001	beta_turn_type_six	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2706805	SO:0001151	SO:0000104	beta_turn_type_six_a	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2885748	SO:0001151	SO:0001411	beta_turn_type_six_a	SO:0000001
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"" []	SO	2706807	SO:0001152	SO:0000839	beta_turn_type_six_a_one	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"" []	SO	2706808	SO:0001152	SO:0000839	beta_turn_type_six_a_one	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	biosapiens	polypeptide	SOFA	biosapiens,SOFA	sequence	"" []	SO	2706809	SO:0001153	SO:0000839	beta_turn_type_six_a_two	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	biosapiens,SOFA	sequence	"" []	SO	2706810	SO:0001153	SO:0000839	beta_turn_type_six_a_two	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2706811	SO:0001154	SO:0000104	beta_turn_type_six_b	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2885754	SO:0001154	SO:0001411	beta_turn_type_six_b	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]	SO	2848920	SO:0001155	SO:0000001	beta_turn_type_eight	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]	SO	2706815	SO:0001156	SO:0000831	DRE_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]	SO	2706816	SO:0001158	SO:0000831	E_box_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2706817	SO:0001159	SO:0000831	DMv5_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]	SO	2706818	SO:0001160	SO:0000831	DMv3_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]	SO	2706819	SO:0001161	SO:0000831	DMv2_motif	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	3034768	SO:0001162	SO:0000001	MTE	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	2706821	SO:0001162	SO:0005836	MTE	SO:0000831
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence TCATTCG." [PMID:16827941]	SO	2706822	SO:0001163	SO:0000831	INR1_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CGGACGT." [PMID:16827941]	SO	2706823	SO:0001164	SO:0000831	DPE1_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A promoter motif with consensus sequence CARCCCT." [PMID:16827941]	SO	2706824	SO:0001165	SO:0000831	DMv1_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]	SO	2706825	SO:0001166	SO:0000831	GAGA_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]	SO	2706826	SO:0001167	SO:0000831	NDM2_motif	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]	SO	2706827	SO:0001168	SO:0000831	NDM3_motif	SO:0001411
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	2706829	SO:0001171	SO:0001411	rRNA_21S	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]	SO	2706830	SO:0001178	SO:0000001	pyrrolysine_tRNA_primary_transcript	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	2706831	SO:0001179	SO:0001411	U3_snoRNA	SO:0000001
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	2706835	SO:0001187	SO:0001411	pseudouridylation_guide_snoRNA	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2706836	SO:0001203	SO:0000001	RNA_polymerase_promoter	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2706837	SO:0001204	SO:0001411	Phage_RNA_Polymerase_Promoter	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2706838	SO:0001205	SO:0000831	SP6_RNA_Polymerase_Promoter	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2706839	SO:0001206	SO:0000831	T3_RNA_Polymerase_Promoter	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2706840	SO:0001207	SO:0000831	T7_RNA_Polymerase_Promoter	SO:0001411
8	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]	SO	2706844	SO:0001222	SO:0000733	silenced_by_histone_methylation	SO:0000400
8	"An attribute describes a quality of sequence." [SO:ke]	\N	sequence_attribute	\N	\N	sequence	"An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]	SO	2706845	SO:0001223	SO:0000733	silenced_by_histone_deacetylation	SO:0000400
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]	SO	2706846	SO:0001258	SO:0000831	octamer_motif	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]	SO	2706849	SO:0001463	SO:0000001	lincRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]	SO	2706850	SO:0001465	SO:0000001	three_prime_UST	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]	SO	2706851	SO:0001466	SO:0000001	five_prime_UST	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	2706852	SO:0001468	SO:0000001	three_prime_RST	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]	SO	2706853	SO:0001469	SO:0000001	five_prime_RST	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2706854	SO:0001482	SO:0001411	shadow_enhancer	SO:0000001
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]	SO	2706858	SO:0001567	SO:0001537	stop_retained_variant	SO:0001060
8	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	2706859	SO:0001583	SO:0001564	missense_variant	SO:0001878
8	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	2706860	SO:0001585	SO:0001576	conservative_missense_variant	SO:0001564
8	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	2706861	SO:0001586	SO:0001576	non_conservative_missense_variant	SO:0001564
8	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]	SO	2706862	SO:0001587	SO:0001564	stop_gained	SO:0001878
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]	SO	2706863	SO:0001589	SO:0001537	frameshift_variant	SO:0001060
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	2706864	SO:0001591	SO:0001878	frame_restoring_variant	SO:0001537
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	2706865	SO:0001592	SO:0001878	minus_1_frameshift_variant	SO:0001537
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"" []	SO	2706866	SO:0001593	SO:0001878	minus_2_frameshift_variant	SO:0001537
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	2706867	SO:0001594	SO:0001878	plus_1_frameshift_variant	SO:0001537
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"" []	SO	2706868	SO:0001595	SO:0001878	plus_2_frameshift_variant	SO:0001537
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	2706869	SO:0001612	SO:0001537	elongated_in_frame_polypeptide_C_terminal	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]	SO	2706870	SO:0001613	SO:0001537	elongated_out_of_frame_polypeptide_C_terminal	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	2706871	SO:0001614	SO:0001537	elongated_in_frame_polypeptide_N_terminal_elongation	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]	SO	2706872	SO:0001615	SO:0001537	elongated_out_of_frame_polypeptide_N_terminal	SO:0001060
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]	SO	2848923	SO:0001626	SO:0001537	incomplete_terminal_codon_variant	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]	SO	2706874	SO:0001650	SO:0001537	inframe_variant	SO:0001060
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	2995387	SO:0001661	SO:0001411	RNA_polymerase_II_TATA_box	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	2706876	SO:0001661	SO:0005836	RNA_polymerase_II_TATA_box	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	2885789	SO:0001662	SO:0001411	RNA_polymerase_III_TATA_box	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	2706878	SO:0001662	SO:0000831	RNA_polymerase_III_TATA_box	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	3034769	SO:0001663	SO:0000001	BREd_motif	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	2706880	SO:0001663	SO:0005836	BREd_motif	SO:0000831
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	3034770	SO:0001664	SO:0000001	DCE	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	2706882	SO:0001664	SO:0005836	DCE	SO:0000831
8	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	2706883	SO:0001665	SO:0001679	DCE_SI	SO:0005836
8	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	2706884	SO:0001666	SO:0001679	DCE_SII	SO:0005836
8	"A region of sequence that is involved in the control of a biological process." [SO:ke]	\N	regulatory_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	2706885	SO:0001667	SO:0001679	DCE_SIII	SO:0005836
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]	SO	2706886	SO:0001668	SO:0000001	proximal_promoter_element	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	2706887	SO:0001669	SO:0000831	RNApol_II_core_promoter	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2706888	SO:0001670	SO:0000001	distal_promoter_element	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2961218	SO:0001671	SO:0000001	bacterial_RNApol_promoter_sigma_70	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2961219	SO:0001672	SO:0000001	bacterial_RNApol_promoter_sigma54	SO:0000110
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	2995394	SO:0001675	SO:0001411	A_box_type_1	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	2706894	SO:0001675	SO:0005836	A_box_type_1	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	2995395	SO:0001676	SO:0001411	A_box_type_2	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	2706896	SO:0001676	SO:0005836	A_box_type_2	SO:0000831
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	3034771	SO:0001677	SO:0000001	intermediate_element	SO:0000110
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	2706898	SO:0001677	SO:0005836	intermediate_element	SO:0000831
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification site where the modification is the methylation of the residue." [SO:ke]	SO	2706900	SO:0001701	SO:0000104	histone_methylation_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification where the modification is the acylation of the residue." [SO:ke]	SO	2706902	SO:0001702	SO:0000104	histone_acetylation_site	SO:0001411
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706904	SO:0001703	SO:0100021	H3K9_acetylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706905	SO:0001704	SO:0100021	H3K14_acetylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706906	SO:0001705	SO:0100021	H3K4_monomethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706907	SO:0001706	SO:0100021	H3K4_trimethylation	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706908	SO:0001707	SO:0100021	H3K9_trimethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706909	SO:0001708	SO:0100021	H3K27_monomethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706910	SO:0001709	SO:0100021	H3K27_trimethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706911	SO:0001710	SO:0100021	H3K79_monomethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706912	SO:0001711	SO:0100021	H3K79_dimethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706913	SO:0001712	SO:0100021	H3K79_trimethylation_site	SO:0000839
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706914	SO:0001713	SO:0000839	H4K20_monomethylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706915	SO:0001713	SO:0000839	H4K20_monomethylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706916	SO:0001714	SO:0000839	H2BK5_monomethylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2706917	SO:0001714	SO:0000839	H2BK5_monomethylation_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification site where ubiquitin may be added." [SO:ke]	SO	2706918	SO:0001716	SO:0000104	histone_ubiqitination_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	2706920	SO:0001717	SO:0000839	H2B_ubiquitination_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	2706921	SO:0001717	SO:0000839	H2B_ubiquitination_site	SO:0001411
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2706922	SO:0001718	SO:0100021	H3K18_acetylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2706923	SO:0001719	SO:0100021	H3K23_acylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2706924	SO:0001721	SO:0100021	H3K27_acylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2706925	SO:0001722	SO:0100021	H3K36_monomethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	2706926	SO:0001723	SO:0100021	H3K36_dimethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	2706927	SO:0001724	SO:0100021	H3K36_trimethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2706928	SO:0001725	SO:0100021	H3K4_dimethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2706929	SO:0001726	SO:0100021	H3K27_dimethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2706930	SO:0001727	SO:0100021	H3K9_monomethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	2706931	SO:0001728	SO:0100021	H3K9_dimethylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2706932	SO:0001729	SO:0100021	H4K16_acylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2706933	SO:0001730	SO:0100021	H4K5_acylation_site	SO:0000839
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	2706934	SO:0001731	SO:0100021	H4K8_acylation_site	SO:0000839
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2706935	SO:0001732	SO:0000839	H3K27_methylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2706936	SO:0001732	SO:0000839	H3K27_methylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2706937	SO:0001733	SO:0000839	H3K36_methylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2706938	SO:0001733	SO:0000839	H3K36_methylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	2706939	SO:0001734	SO:0000839	H3K4_methylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	2706940	SO:0001734	SO:0000839	H3K4_methylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2706941	SO:0001735	SO:0000839	H3K79_methylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2706942	SO:0001735	SO:0000839	H3K79_methylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2706943	SO:0001736	SO:0000839	H3K9_methylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2706944	SO:0001736	SO:0000839	H3K9_methylation_site	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]	SO	2706945	SO:0001737	SO:0000104	histone_acylation_region	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	2706947	SO:0001738	SO:0000839	H4K_acylation_region	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	2706948	SO:0001738	SO:0000839	H4K_acylation_region	SO:0001411
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706949	SO:0001748	SO:0000673	SL3_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995452	SO:0001748	SO:0001411	SL3_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706951	SO:0001749	SO:0000673	SL4_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995453	SO:0001749	SO:0001411	SL4_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706953	SO:0001750	SO:0000673	SL5_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995454	SO:0001750	SO:0001411	SL5_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706955	SO:0001751	SO:0000673	SL6_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995455	SO:0001751	SO:0001411	SL6_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706957	SO:0001752	SO:0000673	SL7_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995456	SO:0001752	SO:0001411	SL7_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706959	SO:0001753	SO:0000673	SL8_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995457	SO:0001753	SO:0001411	SL8_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706961	SO:0001754	SO:0000673	SL9_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995458	SO:0001754	SO:0001411	SL9_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706963	SO:0001755	SO:0000673	SL10_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995459	SO:0001755	SO:0001411	SL10_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706965	SO:0001756	SO:0000673	SL11_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995460	SO:0001756	SO:0001411	SL11_acceptor_site	SO:0000001
8	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2706967	SO:0001757	SO:0000673	SL12_acceptor_site	SO:0000831
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2995461	SO:0001757	SO:0001411	SL12_acceptor_site	SO:0000001
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]	SO	2706971	SO:0001798	SO:0001235	regional_centromere_inner_repeat_region	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]	SO	2706973	SO:0001804	SO:0000104	DDB_box	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]	SO	2706975	SO:0001810	SO:0000104	PIP_box	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]	SO	2848924	SO:0001811	SO:0000001	phosphorylation_site	SO:0000110
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	2706979	SO:0001820	SO:0001878	inframe_indel	SO:0001537
8	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]	SO	2706980	SO:0001821	SO:0001564	inframe_insertion	SO:0001878
8	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]	SO	2706981	SO:0001822	SO:0001564	inframe_deletion	SO:0001878
8	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	2706982	SO:0001823	SO:0001576	conservative_inframe_insertion	SO:0001564
8	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	2706983	SO:0001824	SO:0001576	disruptive_inframe_insertion	SO:0001564
8	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	2706984	SO:0001825	SO:0001576	conservative_inframe_deletion	SO:0001564
8	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	2706985	SO:0001826	SO:0001576	disruptive_inframe_deletion	SO:0001564
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]	SO	2706986	SO:0001835	SO:0000001	N_region	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]	SO	2706987	SO:0001836	SO:0000001	S_region	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]	SO	2706988	SO:0001840	SO:0000001	GATA_box	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]	SO	2706989	SO:0001848	SO:0000001	homol_D_box	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	2706990	SO:0001851	SO:0001411	iron_repressed_GATA_element	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A dinucleotide repeat region composed of GT repeating elements." [SO:ke]	SO	2706991	SO:0001862	SO:0000001	GT_dinucleotide_repeat	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]	SO	2706992	SO:0001863	SO:0000001	GTT_trinucleotide_repeat	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2706994	SO:0001898	SO:0001235	dg_repeat	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]	SO	2706995	SO:0001899	SO:0001235	dh_repeat	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]	SO	2706996	SO:0001901	SO:0000001	AACCCT_box	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]	SO	2706997	SO:0001903	SO:0000001	intronic_lncRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]	SO	2706998	SO:0001904	SO:0000001	antisense_lncRNA	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]	SO	2961222	SO:0001913	SO:0000001	bacterial_RNApol_promoter_sigma_ecf	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]	SO	2707002	SO:0001923	SO:0000001	TERRA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]	SO	2707003	SO:0001924	SO:0000001	ARRET	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]	SO	2707004	SO:0001925	SO:0000001	ARIA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]	SO	2707005	SO:0001926	SO:0000001	anti_ARRET	SO:0000110
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	2707006	SO:0001935	SO:0000839	H3K20_trimethylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	2707007	SO:0001935	SO:0000839	H3K20_trimethylation_site	SO:0001411
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	2707008	SO:0001936	SO:0100021	H3K36_acetylation_site	SO:0000839
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	2707009	SO:0001937	SO:0000839	H2BK12_acetylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	2707010	SO:0001937	SO:0000839	H2BK12_acetylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2707011	SO:0001938	SO:0000839	H2AK5_acetylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2707012	SO:0001938	SO:0000839	H2AK5_acetylation_site	SO:0001411
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2707013	SO:0001939	SO:0100021	H4K12_acetylation_site	SO:0000839
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2707014	SO:0001940	SO:0000839	H2BK120_acetylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2707015	SO:0001940	SO:0000839	H2BK120_acetylation_site	SO:0001411
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2707016	SO:0001941	SO:0100021	H4K91_acetylation_site	SO:0000839
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2707017	SO:0001942	SO:0000839	H2BK20_acetylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2707018	SO:0001942	SO:0000839	H2BK20_acetylation_site	SO:0001411
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2707019	SO:0001943	SO:0100021	H3K4ac_acetylation_site	SO:0000839
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2707020	SO:0001944	SO:0000839	H2AK9_acetylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2707021	SO:0001944	SO:0000839	H2AK9_acetylation_site	SO:0001411
8	"Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]	\N	polypeptide_region	biosapiens,SOFA	biosapiens	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2707022	SO:0001945	SO:0100021	H3K56_acetylation_site	SO:0000839
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2707023	SO:0001946	SO:0000839	H2BK15_acetylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2707024	SO:0001946	SO:0000839	H2BK15_acetylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	2707025	SO:0001947	SO:0000839	H3R2_monomethylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	2707026	SO:0001947	SO:0000839	H3R2_monomethylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2707027	SO:0001948	SO:0000839	H3R2_dimethylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2707028	SO:0001948	SO:0000839	H3R2_dimethylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	2707029	SO:0001949	SO:0000839	H4R3_dimethylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	2707030	SO:0001949	SO:0000839	H4R3_dimethylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	2707031	SO:0001950	SO:0000839	H4K4_trimethylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	2707032	SO:0001950	SO:0000839	H4K4_trimethylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2707033	SO:0001951	SO:0000839	H3K23_dimethylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2707034	SO:0001951	SO:0000839	H3K23_dimethylation_site	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]	SO	2707035	SO:0001959	SO:0000001	TCT_motif	SO:0000110
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2707036	SO:0001972	SO:0000839	histone_4_acylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2707037	SO:0001972	SO:0000839	histone_4_acylation_site	SO:0001411
8	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2707038	SO:0001973	SO:0000839	histone_3_acetylation_site	SO:0000104
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2707039	SO:0001973	SO:0000839	histone_3_acetylation_site	SO:0001411
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]	SO	2707040	SO:0001980	SO:0000001	G_box	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]	SO	2707041	SO:0001981	SO:0000001	L_box	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]	SO	2707042	SO:0001982	SO:0000001	I-box	SO:0000110
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]	SO	2707043	SO:0001983	SO:0001537	5_prime_UTR_premature_start_codon_variant	SO:0001060
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	2707044	SO:0001988	SO:0001878	5_prime_UTR_premature_start_codon_gain_variant	SO:0001537
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	2707045	SO:0001989	SO:0001878	5_prime_UTR_premature_start_codon_loss_variant	SO:0001537
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	2707046	SO:0001990	SO:0001878	five_prime_UTR_premature_start_codon_location_variant	SO:0001537
8	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	2707047	SO:0001992	SO:0001878	nonsynonymous_variant	SO:0001537
8	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2707049	SO:0002008	SO:0001791	rare_amino_acid_variant	SO:0001576
8	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2707050	SO:0002008	SO:0001968	rare_amino_acid_variant	SO:0001576
8	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2707051	SO:0002009	SO:0001580	selenocysteine_loss	SO:0001791
8	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2707052	SO:0002009	SO:0001580	selenocysteine_loss	SO:0001968
8	"A sequence variant that changes exon sequence." [SO:ke]	\N	exon_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2707053	SO:0002010	SO:0001580	pyrrolysine_loss	SO:0001791
8	"A transcript variant of a protein coding gene." [SO:ke]	\N	coding_transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2707054	SO:0002010	SO:0001580	pyrrolysine_loss	SO:0001968
10	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A codon variant that changes at least one base of the canonical start codon." [SO:ke]	SO	2961223	SO:0002012	SO:0001537	start_lost	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]	SO	2707056	SO:0002013	SO:0001537	5_prime_UTR_truncation	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]	SO	2707057	SO:0002014	SO:0001537	5_prime_UTR_elongation	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]	SO	2707058	SO:0002015	SO:0001537	3_prime_UTR_truncation	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]	SO	2707059	SO:0002016	SO:0001537	3_prime_UTR_elongation	SO:0001060
8	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]	SO	2707060	SO:0002019	SO:0001537	start_retained_variant	SO:0001060
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]	SO	2707061	SO:0005837	SO:0000001	U14_snoRNA_primary_transcript	SO:0000110
8	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	2707062	SO:0005841	SO:0001411	methylation_guide_snoRNA	SO:0000001
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]	SO	2707063	SO:0005856	SO:0000001	selenocysteine_tRNA_primary_transcript	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]	SO	2707064	SO:0005857	SO:0000001	selenocysteinyl_tRNA	SO:0000110
8	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	SO	2707066	SO:1000012	SO:0000001	C_to_T_transition_at_pCpG_site	SO:0000110
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]	SO	2707067	SO:1000043	SO:0001026	Robertsonian_fusion	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal inversion that includes the centromere." [FB:reference_manual]	SO	2707068	SO:1000046	SO:0001026	pericentric_inversion	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal inversion that does not include the centromere." [FB:reference_manual]	SO	2707069	SO:1000047	SO:0001026	paracentric_inversion	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]	SO	2707070	SO:1000048	SO:0001026	reciprocal_chromosomal_translocation	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A ring chromosome which is a copy of another chromosome." [SO:ke]	SO	2707071	SO:1000145	SO:0001026	free_ring_duplication	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]	SO	2707072	SO:1000147	SO:0001026	deficient_translocation	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]	SO	2707073	SO:1000150	SO:0001026	cyclic_translocation	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]	SO	2707074	SO:1000151	SO:0001026	bipartite_inversion	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2707075	SO:1000152	SO:0001026	uninverted_insertional_duplication	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	2707076	SO:1000153	SO:0001026	inverted_insertional_duplication	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]	SO	2707077	SO:1000156	SO:0001026	inverted_interchromosomal_transposition	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2707078	SO:1000157	SO:0001026	uninverted_interchromosomal_transposition	SO:0001260
9	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]	SO	2848925	SO:1000158	SO:0001026	inverted_intrachromosomal_transposition	SO:0001260
9	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]	SO	2848926	SO:1000159	SO:0001026	uninverted_intrachromosomal_transposition	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2707081	SO:1000160	SO:0001026	unoriented_insertional_duplication	SO:0001260
8	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2707082	SO:1000161	SO:0001026	unoriented_interchromosomal_transposition	SO:0001260
9	"A collection of discontinuous sequences." [SO:ke]	\N	sequence_collection	\N	\N	sequence	"An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]	SO	2848927	SO:1000162	SO:0001026	unoriented_intrachromosomal_transposition	SO:0001260
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	2707085	SO:1001247	SO:0000831	orphan_CDS	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]	SO	2961224	SO:1001247	SO:0000001	orphan_CDS	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	2848928	SO:1001249	SO:0000831	CDS_supported_by_domain_match_data	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CDS that is supported by domain similarity." [SO:xp]	SO	3034772	SO:1001249	SO:0000001	CDS_supported_by_domain_match_data	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	2848931	SO:1001259	SO:0000831	CDS_supported_by_EST_or_cDNA_data	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A CDS that is supported by similarity to EST or cDNA data." [SO:xp]	SO	3034773	SO:1001259	SO:0000001	CDS_supported_by_EST_or_cDNA_data	SO:0000110
9	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2848933	SO:1001269	SO:0000233	four_bp_start_codon	SO:0000673
9	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2848934	SO:1001269	SO:0000833	four_bp_start_codon	SO:0000673
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2848935	SO:1001269	SO:0000833	four_bp_start_codon	SO:0001411
9	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2848936	SO:1001273	SO:0000233	CTG_start_codon	SO:0000673
9	"An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]	\N	transcript	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2848937	SO:1001273	SO:0000833	CTG_start_codon	SO:0000673
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2848938	SO:1001273	SO:0000833	CTG_start_codon	SO:0001411
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	2707104	SO:1001279	SO:0000831	three_prime_stem_loop_structure	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]	SO	2961227	SO:1001279	SO:0000001	three_prime_stem_loop_structure	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	2707107	SO:1001281	SO:0000831	flanking_three_prime_quadruplet_recoding_signal	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]	SO	2961228	SO:1001281	SO:0000001	flanking_three_prime_quadruplet_recoding_signal	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	2707109	SO:1001282	SO:0000831	UAG_stop_codon_signal	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A stop codon signal for a UAG stop codon redefinition." [SO:ke]	SO	2961229	SO:1001282	SO:0000001	UAG_stop_codon_signal	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	2707111	SO:1001283	SO:0000831	UAA_stop_codon_signal	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A stop codon signal for a UAA stop codon redefinition." [SO:ke]	SO	2961230	SO:1001283	SO:0000001	UAA_stop_codon_signal	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	2707113	SO:1001285	SO:0000831	UGA_stop_codon_signal	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A stop codon signal for a UGA stop codon redefinition." [SO:ke]	SO	2961231	SO:1001285	SO:0000001	UGA_stop_codon_signal	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	2707115	SO:1001286	SO:0000831	three_prime_repeat_recoding_signal	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]	SO	2961232	SO:1001286	SO:0000001	three_prime_repeat_recoding_signal	SO:0000110
8	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	2707117	SO:1001287	SO:0000831	distant_three_prime_recoding_signal	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]	SO	2961233	SO:1001287	SO:0000001	distant_three_prime_recoding_signal	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]	SO	2885606	SO:0000014	SO:0000831	INR_motif	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]	SO	2885607	SO:0000015	SO:0000831	DPE_motif	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]	SO	2885608	SO:0000016	SO:0000831	BREu_motif	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An enhancer bound by a factor." [SO:xp]	SO	2885610	SO:0000166	SO:0000001	enhancer_bound_by_factor	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]	SO	2885611	SO:0000169	SO:0000001	RNApol_I_promoter	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]	SO	2885612	SO:0000170	SO:0000001	RNApol_II_promoter	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]	SO	2885613	SO:0000171	SO:0000001	RNApol_III_promoter	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885616	SO:0000302	SO:0000001	J_gene_recombination_feature	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]	SO	2885619	SO:0000375	SO:0000001	rRNA_5_8S	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	SO	2885620	SO:0000379	SO:0000001	GcvB_RNA	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	SO	2885623	SO:0000403	SO:0000001	U14_snoRNA	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]	SO	2885624	SO:0000407	SO:0000001	rRNA_18S	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885631	SO:0000427	SO:0001037	R_five_prime_LTR_region	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2885632	SO:0000427	SO:0001037	R_five_prime_LTR_region	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885633	SO:0000428	SO:0001037	U5_five_prime_LTR_region	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2885634	SO:0000428	SO:0001037	U5_five_prime_LTR_region	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885635	SO:0000429	SO:0001037	U3_five_prime_LTR_region	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2885636	SO:0000429	SO:0001037	U3_five_prime_LTR_region	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885637	SO:0000430	SO:0001037	R_three_prime_LTR_region	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2885638	SO:0000430	SO:0001037	R_three_prime_LTR_region	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885639	SO:0000431	SO:0001037	U3_three_prime_LTR_region	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2885640	SO:0000431	SO:0001037	U3_three_prime_LTR_region	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885641	SO:0000432	SO:0001037	U5_three_prime_LTR_region	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"" []	SO	2885642	SO:0000432	SO:0001037	U5_three_prime_LTR_region	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885643	SO:0000458	SO:0000001	D_gene_segment	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885644	SO:0000466	SO:0000001	V_gene_segment	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885645	SO:0000470	SO:0000001	J_gene_segment	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885646	SO:0000478	SO:0000001	C_gene_segment	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885647	SO:0000485	SO:0000001	DJ_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885648	SO:0000487	SO:0000001	VDJ_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885649	SO:0000488	SO:0000001	VDJ_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885650	SO:0000489	SO:0000001	VJ_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885651	SO:0000490	SO:0000001	VJ_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885652	SO:0000491	SO:0000001	VJ_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2885653	SO:0000492	SO:0000001	D_gene_recombination_feature	SO:0000110
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2981284	SO:0000493	SO:0001411	three_prime_D_heptamer	SO:0000001
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2981285	SO:0000494	SO:0001411	three_prime_D_nonamer	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	3044100	SO:0000495	SO:0000001	three_prime_D_spacer	SO:0000110
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2981286	SO:0000496	SO:0001411	five_prime_D_heptamer	SO:0000001
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2981287	SO:0000497	SO:0001411	five_prime_D_nonamer	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	3044101	SO:0000498	SO:0000001	five_prime_D_spacer	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885660	SO:0000504	SO:0000001	D_DJ_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885661	SO:0000505	SO:0000001	D_DJ_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885662	SO:0000506	SO:0000001	D_DJ_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885663	SO:0000508	SO:0000001	D_DJ_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885664	SO:0000509	SO:0000001	D_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885665	SO:0000510	SO:0000001	VD_gene_segment	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885666	SO:0000511	SO:0000001	J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885667	SO:0000513	SO:0000001	J_cluster	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885668	SO:0000514	SO:0001411	J_nonamer	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885669	SO:0000515	SO:0001411	J_heptamer	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2981288	SO:0000517	SO:0000001	J_spacer	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885671	SO:0000518	SO:0000001	V_DJ_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885672	SO:0000519	SO:0000001	V_DJ_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885673	SO:0000520	SO:0000001	V_VDJ_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885674	SO:0000521	SO:0000001	V_VDJ_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885675	SO:0000522	SO:0000001	V_VDJ_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885676	SO:0000523	SO:0000001	V_VJ_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885677	SO:0000524	SO:0000001	V_VJ_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885678	SO:0000525	SO:0000001	V_VJ_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885679	SO:0000526	SO:0000001	V_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885680	SO:0000527	SO:0000001	V_D_DJ_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885681	SO:0000528	SO:0000001	V_D_DJ_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885682	SO:0000529	SO:0000001	V_D_DJ_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885683	SO:0000530	SO:0000001	V_D_DJ_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885684	SO:0000531	SO:0000001	V_D_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885685	SO:0000532	SO:0000001	V_D_J_cluster	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885686	SO:0000533	SO:0001411	V_heptamer	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885687	SO:0000534	SO:0000001	V_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885688	SO:0000535	SO:0000001	V_J_C_cluster	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885689	SO:0000536	SO:0001411	V_nonamer	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2981289	SO:0000537	SO:0000001	V_spacer	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885691	SO:0000538	SO:0000001	V_gene_recombination_feature	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885692	SO:0000539	SO:0000001	DJ_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885693	SO:0000540	SO:0000001	DJ_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885694	SO:0000541	SO:0000001	VDJ_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885695	SO:0000542	SO:0000001	V_DJ_C_cluster	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885696	SO:0000556	SO:0001411	five_prime_D_recombination_signal_sequence	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885697	SO:0000558	SO:0000001	C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885698	SO:0000559	SO:0000001	D_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885699	SO:0000560	SO:0000001	D_J_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885700	SO:0000561	SO:0000001	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2885701	SO:0000562	SO:0000001	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885702	SO:0000564	SO:0000001	V_DJ_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885703	SO:0000565	SO:0000001	V_VDJ_J_C_cluster	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885704	SO:0000566	SO:0000001	V_VJ_J_C_cluster	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885705	SO:0000570	SO:0001411	three_prime_D_recombination_signal_sequence	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885706	SO:0000572	SO:0000001	DJ_gene_segment	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885707	SO:0000574	SO:0000001	VDJ_gene_segment	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2885708	SO:0000576	SO:0000001	VJ_gene_segment	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885709	SO:0000617	SO:0001411	RNApol_III_promoter_type_1	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885710	SO:0000618	SO:0001411	RNApol_III_promoter_type_2	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]	SO	2885711	SO:0000620	SO:0000831	B_box	SO:0001411
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"" []	SO	2885712	SO:0000621	SO:0001411	RNApol_III_promoter_type_3	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]	SO	2885713	SO:0000622	SO:0000831	C_box	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	SO	2885714	SO:0000652	SO:0000001	rRNA_5S	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A component of the large ribosomal subunit." [SO:ke]	SO	2885715	SO:0000653	SO:0000001	rRNA_28S	SO:0000110
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	2981290	SO:0000680	SO:0000831	non_canonical_start_codon	SO:0001411
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A start codon that is not the usual AUG sequence." [SO:ke]	SO	3080149	SO:0000680	SO:0000001	non_canonical_start_codon	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2885722	SO:0000685	SO:0000001	DNAseI_hypersensitive_site	SO:0000110
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	2981292	SO:0000883	SO:0000831	stop_codon_read_through	SO:0001411
12	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A stop codon redefined to be a new amino acid." [SO:ke]	SO	3080150	SO:0000883	SO:0000001	stop_codon_read_through	SO:0000110
10	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	2981294	SO:0000884	SO:0000673	stop_codon_redefined_as_pyrrolysine	SO:0000831
12	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	3087015	SO:0000884	SO:0001411	stop_codon_redefined_as_pyrrolysine	SO:0000001
10	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	2981296	SO:0000885	SO:0000673	stop_codon_redefined_as_selenocysteine	SO:0000831
12	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	3087016	SO:0000885	SO:0001411	stop_codon_redefined_as_selenocysteine	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]	SO	2885735	SO:0001000	SO:0000001	rRNA_16S	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]	SO	2885736	SO:0001001	SO:0000001	rRNA_23S	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	SOFA	sequence_feature	SOFA	SOFA	sequence	"A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]	SO	2885737	SO:0001002	SO:0000001	rRNA_25S	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2981298	SO:0001151	SO:0000001	beta_turn_type_six_a	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"" []	SO	2885750	SO:0001152	SO:0000104	beta_turn_type_six_a_one	SO:0001411
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"" []	SO	2995376	SO:0001152	SO:0001411	beta_turn_type_six_a_one	SO:0000001
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	biosapiens	biological_region	SOFA	SOFA	sequence	"" []	SO	2885752	SO:0001153	SO:0000104	beta_turn_type_six_a_two	SO:0001411
10	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	biosapiens	region	SOFA	SOFA	sequence	"" []	SO	2995378	SO:0001153	SO:0001411	beta_turn_type_six_a_two	SO:0000001
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]	SO	2981299	SO:0001154	SO:0000001	beta_turn_type_six_b	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]	SO	2885761	SO:0001162	SO:0000831	MTE	SO:0001411
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]	SO	2885768	SO:0001171	SO:0000001	rRNA_21S	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	SO	2885769	SO:0001179	SO:0000001	U3_snoRNA	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	2885770	SO:0001187	SO:0000001	pseudouridylation_guide_snoRNA	SO:0000110
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2885771	SO:0001204	SO:0000001	Phage_RNA_Polymerase_Promoter	SO:0000110
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2885772	SO:0001205	SO:0001411	SP6_RNA_Polymerase_Promoter	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2885773	SO:0001206	SO:0001411	T3_RNA_Polymerase_Promoter	SO:0000001
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2885774	SO:0001207	SO:0001411	T7_RNA_Polymerase_Promoter	SO:0000001
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2885776	SO:0001482	SO:0000001	shadow_enhancer	SO:0000110
9	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	2885777	SO:0001583	SO:0001878	missense_variant	SO:0001537
9	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	2885778	SO:0001585	SO:0001564	conservative_missense_variant	SO:0001878
9	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	2885779	SO:0001586	SO:0001564	non_conservative_missense_variant	SO:0001878
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]	SO	2885781	SO:0001591	SO:0001537	frame_restoring_variant	SO:0001060
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	2885782	SO:0001592	SO:0001537	minus_1_frameshift_variant	SO:0001060
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"" []	SO	2885783	SO:0001593	SO:0001537	minus_2_frameshift_variant	SO:0001060
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	SO	2885784	SO:0001594	SO:0001537	plus_1_frameshift_variant	SO:0001060
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"" []	SO	2885785	SO:0001595	SO:0001537	plus_2_frameshift_variant	SO:0001060
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	3044104	SO:0001661	SO:0000001	RNA_polymerase_II_TATA_box	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]	SO	2885787	SO:0001661	SO:0000831	RNA_polymerase_II_TATA_box	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]	SO	2981300	SO:0001662	SO:0000001	RNA_polymerase_III_TATA_box	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]	SO	2885790	SO:0001663	SO:0000831	BREd_motif	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]	SO	2885791	SO:0001664	SO:0000831	DCE	SO:0001411
9	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	2885792	SO:0001665	SO:0005836	DCE_SI	SO:0000831
9	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	2885793	SO:0001666	SO:0005836	DCE_SII	SO:0000831
9	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	2885794	SO:0001667	SO:0005836	DCE_SIII	SO:0000831
9	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	2885795	SO:0001669	SO:0001411	RNApol_II_core_promoter	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	3044105	SO:0001675	SO:0000001	A_box_type_1	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 1 promoter." [SO:ke]	SO	2885797	SO:0001675	SO:0000831	A_box_type_1	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	3044106	SO:0001676	SO:0000001	A_box_type_2	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"An A box within an RNA polymerase III type 2 promoter." [SO:ke]	SO	2885799	SO:0001676	SO:0000831	A_box_type_2	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]	SO	2885800	SO:0001677	SO:0000831	intermediate_element	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885803	SO:0001703	SO:0000839	H3K9_acetylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885804	SO:0001703	SO:0000839	H3K9_acetylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885805	SO:0001704	SO:0000839	H3K14_acetylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885806	SO:0001704	SO:0000839	H3K14_acetylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885807	SO:0001705	SO:0000839	H3K4_monomethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885808	SO:0001705	SO:0000839	H3K4_monomethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885809	SO:0001706	SO:0000839	H3K4_trimethylation	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885810	SO:0001706	SO:0000839	H3K4_trimethylation	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885811	SO:0001707	SO:0000839	H3K9_trimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885812	SO:0001707	SO:0000839	H3K9_trimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885813	SO:0001708	SO:0000839	H3K27_monomethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885814	SO:0001708	SO:0000839	H3K27_monomethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885815	SO:0001709	SO:0000839	H3K27_trimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885816	SO:0001709	SO:0000839	H3K27_trimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885817	SO:0001710	SO:0000839	H3K79_monomethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885818	SO:0001710	SO:0000839	H3K79_monomethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885819	SO:0001711	SO:0000839	H3K79_dimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885820	SO:0001711	SO:0000839	H3K79_dimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885821	SO:0001712	SO:0000839	H3K79_trimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885822	SO:0001712	SO:0000839	H3K79_trimethylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885823	SO:0001713	SO:0000104	H4K20_monomethylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2885825	SO:0001714	SO:0000104	H2BK5_monomethylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone modification site on H2B where ubiquitin may be added." [SO:ke]	SO	2885828	SO:0001717	SO:0000104	H2B_ubiquitination_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2885830	SO:0001718	SO:0000839	H3K18_acetylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2885831	SO:0001718	SO:0000839	H3K18_acetylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2885832	SO:0001719	SO:0000839	H3K23_acylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2885833	SO:0001719	SO:0000839	H3K23_acylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2885834	SO:0001721	SO:0000839	H3K27_acylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2885835	SO:0001721	SO:0000839	H3K27_acylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2885836	SO:0001722	SO:0000839	H3K36_monomethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2885837	SO:0001722	SO:0000839	H3K36_monomethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	2885838	SO:0001723	SO:0000839	H3K36_dimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	2885839	SO:0001723	SO:0000839	H3K36_dimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	2885840	SO:0001724	SO:0000839	H3K36_trimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	2885841	SO:0001724	SO:0000839	H3K36_trimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2885842	SO:0001725	SO:0000839	H3K4_dimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2885843	SO:0001725	SO:0000839	H3K4_dimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2885844	SO:0001726	SO:0000839	H3K27_dimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2885845	SO:0001726	SO:0000839	H3K27_dimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2885846	SO:0001727	SO:0000839	H3K9_monomethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2885847	SO:0001727	SO:0000839	H3K9_monomethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	2885848	SO:0001728	SO:0000839	H3K9_dimethylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	2885849	SO:0001728	SO:0000839	H3K9_dimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2885850	SO:0001729	SO:0000839	H4K16_acylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2885851	SO:0001729	SO:0000839	H4K16_acylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2885852	SO:0001730	SO:0000839	H4K5_acylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2885853	SO:0001730	SO:0000839	H4K5_acylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	2885854	SO:0001731	SO:0000839	H4K8_acylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	2885855	SO:0001731	SO:0000839	H4K8_acylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2885856	SO:0001732	SO:0000104	H3K27_methylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2885858	SO:0001733	SO:0000104	H3K36_methylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]	SO	2885860	SO:0001734	SO:0000104	H3K4_methylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2885862	SO:0001735	SO:0000104	H3K79_methylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]	SO	2885864	SO:0001736	SO:0000104	H3K9_methylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]	SO	2885867	SO:0001738	SO:0000104	H4K_acylation_region	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885869	SO:0001748	SO:0000831	SL3_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044107	SO:0001748	SO:0000001	SL3_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885871	SO:0001749	SO:0000831	SL4_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044108	SO:0001749	SO:0000001	SL4_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885873	SO:0001750	SO:0000831	SL5_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044109	SO:0001750	SO:0000001	SL5_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885875	SO:0001751	SO:0000831	SL6_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044110	SO:0001751	SO:0000001	SL6_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885877	SO:0001752	SO:0000831	SL7_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044111	SO:0001752	SO:0000001	SL7_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885879	SO:0001753	SO:0000831	SL8_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044112	SO:0001753	SO:0000001	SL8_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885881	SO:0001754	SO:0000831	SL9_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044113	SO:0001754	SO:0000001	SL9_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885883	SO:0001755	SO:0000831	SL10_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044114	SO:0001755	SO:0000001	SL10_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885885	SO:0001756	SO:0000831	SL11_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044115	SO:0001756	SO:0000001	SL11_acceptor_site	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	2885887	SO:0001757	SO:0000831	SL12_acceptor_site	SO:0001411
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]	SO	3044116	SO:0001757	SO:0000001	SL12_acceptor_site	SO:0000110
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]	SO	2885892	SO:0001820	SO:0001537	inframe_indel	SO:0001060
9	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]	SO	2885895	SO:0001823	SO:0001564	conservative_inframe_insertion	SO:0001878
9	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]	SO	2885896	SO:0001824	SO:0001564	disruptive_inframe_insertion	SO:0001878
9	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]	SO	2885897	SO:0001825	SO:0001564	conservative_inframe_deletion	SO:0001878
9	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]	SO	2885898	SO:0001826	SO:0001564	disruptive_inframe_deletion	SO:0001878
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]	SO	2885899	SO:0001851	SO:0000001	iron_repressed_GATA_element	SO:0000110
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]	SO	2885902	SO:0001935	SO:0000104	H3K20_trimethylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	2885904	SO:0001936	SO:0000839	H3K36_acetylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	2885905	SO:0001936	SO:0000839	H3K36_acetylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]	SO	2885906	SO:0001937	SO:0000104	H2BK12_acetylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2885908	SO:0001938	SO:0000104	H2AK5_acetylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2885910	SO:0001939	SO:0000839	H4K12_acetylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2885911	SO:0001939	SO:0000839	H4K12_acetylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2885912	SO:0001940	SO:0000104	H2BK120_acetylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2885914	SO:0001941	SO:0000839	H4K91_acetylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2885915	SO:0001941	SO:0000839	H4K91_acetylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2885916	SO:0001942	SO:0000104	H2BK20_acetylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2885918	SO:0001943	SO:0000839	H3K4ac_acetylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2885919	SO:0001943	SO:0000839	H3K4ac_acetylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]	SO	2885920	SO:0001944	SO:0000104	H2AK9_acetylation_site	SO:0001411
9	"A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]	\N	polypeptide	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2885922	SO:0001945	SO:0000839	H3K56_acetylation_site	SO:0000104
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	biosapiens,SOFA	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2885923	SO:0001945	SO:0000839	H3K56_acetylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]	SO	2885924	SO:0001946	SO:0000104	H2BK15_acetylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]	SO	2885926	SO:0001947	SO:0000104	H3R2_monomethylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2885928	SO:0001948	SO:0000104	H3R2_dimethylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]	SO	2885930	SO:0001949	SO:0000104	H4R3_dimethylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]	SO	2885932	SO:0001950	SO:0000104	H4K4_trimethylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]	SO	2885934	SO:0001951	SO:0000104	H3K23_dimethylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2885936	SO:0001972	SO:0000104	histone_4_acylation_site	SO:0001411
9	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]	SO	2885938	SO:0001973	SO:0000104	histone_3_acetylation_site	SO:0001411
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is gained." [Sanger:am]	SO	2885940	SO:0001988	SO:0001537	5_prime_UTR_premature_start_codon_gain_variant	SO:0001060
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is lost." [SANGER:am]	SO	2885941	SO:0001989	SO:0001537	5_prime_UTR_premature_start_codon_loss_variant	SO:0001060
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A 5' UTR variant where a premature start codon is moved." [SANGER:am]	SO	2885942	SO:0001990	SO:0001537	five_prime_UTR_premature_start_codon_location_variant	SO:0001060
9	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]	SO	2885943	SO:0001992	SO:0001537	nonsynonymous_variant	SO:0001060
9	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2885944	SO:0002008	SO:0001576	rare_amino_acid_variant	SO:0001564
9	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2885945	SO:0002009	SO:0001791	selenocysteine_loss	SO:0001576
9	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2885946	SO:0002009	SO:0001968	selenocysteine_loss	SO:0001576
9	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2885947	SO:0002010	SO:0001791	pyrrolysine_loss	SO:0001576
9	"A sequence variant that changes the structure of the transcript." [SO:ke]	\N	transcript_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2885948	SO:0002010	SO:0001968	pyrrolysine_loss	SO:0001576
9	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]	SO	2885949	SO:0005841	SO:0000001	methylation_guide_snoRNA	SO:0000110
10	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	2981303	SO:1001269	SO:0000673	four_bp_start_codon	SO:0000831
12	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	3087017	SO:1001269	SO:0001411	four_bp_start_codon	SO:0000001
10	"A region of a gene." [SO:ke]	\N	gene_member_region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	2981305	SO:1001273	SO:0000673	CTG_start_codon	SO:0000831
12	"A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]	\N	region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	3087018	SO:1001273	SO:0001411	CTG_start_codon	SO:0000001
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	3052360	SO:0000493	SO:0000001	three_prime_D_heptamer	SO:0000110
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	3052361	SO:0000494	SO:0000001	three_prime_D_nonamer	SO:0000110
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	3052362	SO:0000496	SO:0000001	five_prime_D_heptamer	SO:0000110
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	3052363	SO:0000497	SO:0000001	five_prime_D_nonamer	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2995359	SO:0000514	SO:0000001	J_nonamer	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2995360	SO:0000515	SO:0000001	J_heptamer	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2995361	SO:0000533	SO:0000001	V_heptamer	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2995362	SO:0000536	SO:0000001	V_nonamer	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2995363	SO:0000556	SO:0000001	five_prime_D_recombination_signal_sequence	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	SO	2995364	SO:0000570	SO:0000001	three_prime_D_recombination_signal_sequence	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2995365	SO:0000617	SO:0000001	RNApol_III_promoter_type_1	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2995366	SO:0000618	SO:0000001	RNApol_III_promoter_type_2	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"" []	SO	2995368	SO:0000621	SO:0000001	RNApol_III_promoter_type_3	SO:0000110
11	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	3052366	SO:0000884	SO:0000831	stop_codon_redefined_as_pyrrolysine	SO:0001411
13	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]	SO	3100511	SO:0000884	SO:0000001	stop_codon_redefined_as_pyrrolysine	SO:0000110
11	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	3052368	SO:0000885	SO:0000831	stop_codon_redefined_as_selenocysteine	SO:0001411
13	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]	SO	3100512	SO:0000885	SO:0000001	stop_codon_redefined_as_selenocysteine	SO:0000110
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"" []	SO	3052370	SO:0001152	SO:0000001	beta_turn_type_six_a_one	SO:0000110
11	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	biosapiens	sequence_feature	SOFA	SOFA	sequence	"" []	SO	3052371	SO:0001153	SO:0000001	beta_turn_type_six_a_two	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2995381	SO:0001205	SO:0000001	SP6_RNA_Polymerase_Promoter	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2995382	SO:0001206	SO:0000001	T3_RNA_Polymerase_Promoter	SO:0000110
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]	SO	2995383	SO:0001207	SO:0000001	T7_RNA_Polymerase_Promoter	SO:0000110
10	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]	SO	2995384	SO:0001583	SO:0001537	missense_variant	SO:0001060
10	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	2995385	SO:0001585	SO:0001878	conservative_missense_variant	SO:0001537
10	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	2995386	SO:0001586	SO:0001878	non_conservative_missense_variant	SO:0001537
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]	SO	2995390	SO:0001665	SO:0000831	DCE_SI	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]	SO	2995391	SO:0001666	SO:0000831	DCE_SII	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]	SO	2995392	SO:0001667	SO:0000831	DCE_SIII	SO:0001411
10	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]	SO	2995393	SO:0001669	SO:0000001	RNApol_II_core_promoter	SO:0000110
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995397	SO:0001703	SO:0000104	H3K9_acetylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995399	SO:0001704	SO:0000104	H3K14_acetylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995401	SO:0001705	SO:0000104	H3K4_monomethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995403	SO:0001706	SO:0000104	H3K4_trimethylation	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995405	SO:0001707	SO:0000104	H3K9_trimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995407	SO:0001708	SO:0000104	H3K27_monomethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995409	SO:0001709	SO:0000104	H3K27_trimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995411	SO:0001710	SO:0000104	H3K79_monomethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995413	SO:0001711	SO:0000104	H3K79_dimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]	SO	2995415	SO:0001712	SO:0000104	H3K79_trimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2995420	SO:0001718	SO:0000104	H3K18_acetylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2995422	SO:0001719	SO:0000104	H3K23_acylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]	SO	2995424	SO:0001721	SO:0000104	H3K27_acylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2995426	SO:0001722	SO:0000104	H3K36_monomethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]	SO	2995428	SO:0001723	SO:0000104	H3K36_dimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]	SO	2995430	SO:0001724	SO:0000104	H3K36_trimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2995432	SO:0001725	SO:0000104	H3K4_dimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]	SO	2995434	SO:0001726	SO:0000104	H3K27_dimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]	SO	2995436	SO:0001727	SO:0000104	H3K9_monomethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]	SO	2995438	SO:0001728	SO:0000104	H3K9_dimethylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2995440	SO:0001729	SO:0000104	H4K16_acylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]	SO	2995442	SO:0001730	SO:0000104	H4K5_acylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]	SO	2995444	SO:0001731	SO:0000104	H4K8_acylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]	SO	2995467	SO:0001936	SO:0000104	H3K36_acetylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2995471	SO:0001939	SO:0000104	H4K12_acetylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]	SO	2995474	SO:0001941	SO:0000104	H4K91_acetylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2995477	SO:0001943	SO:0000104	H3K4ac_acetylation_site	SO:0001411
10	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]	SO	2995480	SO:0001945	SO:0000104	H3K56_acetylation_site	SO:0001411
10	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2995490	SO:0002008	SO:0001564	rare_amino_acid_variant	SO:0001878
10	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2995491	SO:0002009	SO:0001576	selenocysteine_loss	SO:0001564
10	"A sequence variant where the structure of the gene is changed." [SO:ke]	\N	gene_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	2995492	SO:0002010	SO:0001576	pyrrolysine_loss	SO:0001564
11	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	3052372	SO:1001269	SO:0000831	four_bp_start_codon	SO:0001411
13	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-canonical start codon with 4 base pairs." [SO:ke]	SO	3100513	SO:1001269	SO:0000001	four_bp_start_codon	SO:0000110
11	"A region defined by its disposition to be involved in a biological process." [SO:cb]	\N	biological_region	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	3052374	SO:1001273	SO:0000831	CTG_start_codon	SO:0001411
13	"Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]	\N	sequence_feature	SOFA	SOFA	sequence	"A non-canonical start codon of sequence CTG." [SO:ke]	SO	3100514	SO:1001273	SO:0000001	CTG_start_codon	SO:0000110
11	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]	SO	3056746	SO:0001585	SO:0001537	conservative_missense_variant	SO:0001060
11	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]	SO	3056747	SO:0001586	SO:0001537	non_conservative_missense_variant	SO:0001060
11	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	3056779	SO:0002008	SO:0001878	rare_amino_acid_variant	SO:0001537
11	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	3056780	SO:0002009	SO:0001564	selenocysteine_loss	SO:0001878
11	"A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]	\N	feature_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	3056781	SO:0002010	SO:0001564	pyrrolysine_loss	SO:0001878
12	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]	SO	3088316	SO:0002008	SO:0001537	rare_amino_acid_variant	SO:0001060
12	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	3088317	SO:0002009	SO:0001878	selenocysteine_loss	SO:0001537
12	"A sequence variant that changes one or more sequence features." [SO:ke]	\N	structural_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	3088318	SO:0002010	SO:0001878	pyrrolysine_loss	SO:0001537
13	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]	SO	3103144	SO:0002009	SO:0001537	selenocysteine_loss	SO:0001060
13	"A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]	\N	sequence_variant	\N	\N	sequence	"A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]	SO	3103145	SO:0002010	SO:0001537	pyrrolysine_loss	SO:0001060
