6	AGI Repeat sequences	repeats-AGI	1	\N
116	Alignments of EST clusters (Unigenes, Gene Indices) from Arabidopsis	EST Cluster (Arabidopsis)	1	{"type": "cdna"}
890	<a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml">Conserved Domain Database</a> models.	CDD	1	{"type": "domain"}
633	Covariance models from <a href='http://rfam.xfam.org'>Rfam</a> (release 12.2), aligned to the genome with 'cmscan' from the <a href='http://eddylab.org/infernal'>Infernal</a> suite of programs. Models are restricted to those observed in species that share a last common ancestor (LCA).	Rfam Models (LCA)	1	{"type": "rna"}
188	Density of coding genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.)	Coding genes (density)	1	\N
117	Alignmments of EST clusters (Unigenes, Gene Indices) from all dicot species	EST Cluster (Dicot)	1	{"type": "cdna"}
635	Dust is a program that identifies low-complexity sequences (regions of the genome with a biased distribution of nucleotides, such as a repeat). The Dust module is widely used with BLAST to prevent 'sticky' regions from determining false hits.	Low complexity (Dust)	1	\N
133	Ab initio prediction of protein coding genes, based on the genomic sequence alone <a rel="external" href="http://europepmc.org/abstract/MED/10779491">AA Salamov et al., Genome Res. 2000 4:516-22</a>.	FGENESH prediction	1	{"caption": "FGENESH prediction", "colour_key": "[biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "fgenesh", "label_key": "[biotype]", "multi_name": "FGENESH prediction", "name": "FGENESH prediction"}
914	<a href="http://www.cathdb.info/">CATH/Gene3D</a> families.	Gene3D	1	{"type": "domain"}
150	Gene annotation by <a href="http://rice.genomics.org.cn">BGI</a> through a process of automatic and manual curation	Genes	1	{"caption": "BGI gene", "colour_key": "[biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "ensembl", "label_key": "[biotype]", "multi_name": "BGI Genes", "name": "BGI Genes"}
917	\N	GOA annotation	0	\N
669	GO term derived transitively from a UniProt record	UniProt-derived GO term	0	\N
425	The Gene Ontology XRef projection pipeline	GO projected xrefs	0	\N
721	Gene encoding an enzyme annotated at the <a rel="external" href="https://plantreactome.gramene.org">Plant Reactome</a>.	Plant Reactome	1	\N
894	<a href="http://hamap.expasy.org/">HAMAP</a> families.	HAMAP	1	{"type": "domain"}
892	<a href="http://www.pantherdb.org/">PANTHER</a> families.	PANTHER	1	{"type": "domain"}
912	InterPro2GO mapping, defined by InterPro.	InterPro2GO mapping	0	\N
225	Density of long non-coding RNA genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.)	Long non-coding genes (density)	1	\N
120	Alignments of EST clusters (Unigenes, Gene Indices) from Maize	EST Cluster (Maize)	1	{"type": "cdna"}
131	Genic nonCoding microsatellites	Marker (microsat)	1	\N
641	RNA genes imported from <a href='http://www.mirbase.org/'>miRBase</a> .	RNA genes	1	{"label_key": "[biotype]", "caption": "Genes", "colour_key": "[biotype]", "default": {"cytoview": "gene_label", "MultiBottom": "collapsed_label", "alignsliceviewbottom": "as_collapsed_label", "MultiTop": "gene_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label"}, "name": "Genes", "key": "ensembl"}
902	Intrinsically disordered regions predicted by <a href="http://protein.bio.unipd.it/mobidblite/">MobiDB lite</a>.	MobiDB lite	1	{"type": "feature"}
118	Alignments of EST clusters (Unigenes, Gene Indices) from monocot species	EST Cluster (Monocot)	1	{"type": "cdna"}
903	Coiled-coil regions predicted by <a rel="external" href="http://www.sciencemag.org/cgi/reprint/252/5009/1162">Ncoils</a>.	Coiled-coils (Ncoils)	1	{"type": "feature"}
189	Density of non-coding RNA genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.)	Non-coding genes (density)	1	\N
127	Genomic location of <a rel="external" href="www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechOvergo.shtml">Overgo</a> probe markers	Overgo Probes	1	\N
169	Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.)	Repeats (percent)	1	\N
168	Percentage of G/C bases in the sequence.	GC content	1	\N
893	Protein domains and motifs from the <a rel="external" href="http://pfam.xfam.org">Pfam</a> database.	Pfam	1	{"type": "domain"}
911	Protein domains and motifs from the <a rel="external" href="http://prosite.expasy.org">PROSITE</a> profiles database.	PROSITE profiles	1	{"type": "domain"}
896	Protein domains and motifs from the <a rel="external" href="http://pir.georgetown.edu">PIR (Protein Information Resource)</a> Superfamily database.	PIRSF	1	{"type": "domain"}
897	Protein fingerprints (groups of conserved motifs) from the <a href="http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/index.php">PRINTS</a> database.	Prints	1	{"type": "domain"}
190	Density of pseudogenes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.)	Pseudogenes (density)	1	\N
637	Repeats detected using the <a href="http://mips.helmholtz-muenchen.de/plant/recat/">MIPS Repeat Database</a> (REdat) using <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a>.	Repeats: REdat	1	\N
638	Repeats identified by <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a>, using the <a rel="external" href="http://www.girinst.org/repbase/">Repbase</a> library of repeat profiles.	Repeats: Repbase	1	\N
642	RNA genes produced by filtering alignments of <a href='http://rfam.xfam.org'>Rfam</a> (release 12.2) covariance models.	RNA genes	1	{"label_key": "[biotype]", "caption": "Genes", "colour_key": "[biotype]", "default": {"cytoview": "gene_label", "MultiBottom": "collapsed_label", "alignsliceviewbottom": "as_collapsed_label", "MultiTop": "gene_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label"}, "name": "Genes", "key": "ensembl"}
123	Genomics location of RFLP (restriction fragment length polymorphism) markers	Marker (RFLP)	1	\N
121	Genomic alignments of rice (Oryza) "Expressed Sequence Tags" (ESTs) from <a rel="external" href="http://www.ncbi.nlm.nih.gov/dbEST/">dbEST</a>	Rice ESTs	1	{"gene": {"do_not_display": "1"}, "type": "est"}
119	Alignments of EST clusters (Unigenes, Gene Indices) from rice (Oryza) species	EST Cluster (Rice)	1	{"type": "cdna"}
913	Protein domains and motifs from the <a rel="external" href="http://prosite.expasy.org">PROSITE</a> patterns database.	PROSITE patterns	1	{"type": "domain"}
906	Low complexity peptide sequences identified by <a rel="external" href="http://www.biology.wustl.edu/gcg/seg.html">Seg</a>.	Low complexity (Seg)	1	{"type": "feature"}
899	<a href="http://sfld.rbvi.ucsf.edu/">Structure-Function Linkage Database</a> families.	SFLD	1	{"type": "domain"}
224	Density of short non-coding RNA genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.)	Short non-coding genes (density)	1	\N
904	Signal peptide cleavage sites predicted by <a rel="external" href="http://www.cbs.dtu.dk/services/SignalP">SignalP</a>.	Cleavage site (Signalp)	1	{"type": "feature"}
900	Protein domains and motifs from the <a rel="external" href="http://smart.embl-heidelberg.de">SMART</a> database.	SMART	1	{"type": "domain"}
149	Density of single nucleotide polymorphisms (SNPs), calculated by dividing the chromosome into 150 "bins" and counting the SNPs in each. (For very short chromosomes, e.g. MT, some SNPs contribute to multiple bins.)	SNP Density	1	\N
901	Protein domains and motifs from the <a rel="external" href="http://supfam.org/SUPERFAMILY">SUPERFAMILY</a> database.	Superfamily	1	{"type": "domain"}
122	Locations of <a rel="external" href="http://en.wikipedia.org/wiki/T-DNA">T-DNA</A> and transposable element insertion sites identified via alignment to the genome of appropriate flanking sequence tags (FST)	Insertion Sites	1	\N
907	Protein domains and motifs from the <a rel="external" href="http://www.jcvi.org/cgi-bin/tigrfams/index.cgi">TIGRFAM</a> database.	TIGRFAM	1	{"type": "domain"}
905	Transmembrane helices predicted by <a rel="external" href="http://www.cbs.dtu.dk/~krogh/TMHMM">TMHMM</a>.	Transmembrane helices	1	{"type": "feature"}
636	<a rel="external" href="https://tandem.bu.edu/trf/trf.html">Tandem Repeats Finder</a> locates adjacent copies of a pattern of nucleotides.	Tandem repeats (TRF)	1	\N
634	tRNA models predicted with <a href="http://lowelab.ucsc.edu/tRNAscan-SE">tRNAscan-SE</a> (release 1.3.1).	tRNA Models	1	{"type": "rna"}
643	RNA genes produced by filtering predictions from <a href='http://lowelab.ucsc.edu/tRNAscan-SE/'>tRNAscan-SE</a> v1.23.	RNA genes	1	{"label_key": "[biotype]", "caption": "Genes", "colour_key": "[biotype]", "default": {"cytoview": "gene_label", "MultiBottom": "collapsed_label", "alignsliceviewbottom": "as_collapsed_label", "MultiTop": "gene_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label"}, "name": "Genes", "key": "ensembl"}
667	UniParc mapping based on sequence checksums	UniParc cross-reference	0	\N
164	Sequences from various databases are matched to Ensembl transcripts using <a rel="external" href="http://www.biomedcentral.com/1471-2105/6/31">Exonerate</a>. These are external references, or 'Xrefs'.	DNA match	0	\N
165	match	Protein	0	\N
668	UniProt cross-reference derived transitively from a UniParc identifier	UniParc-derived cross-reference	0	\N
670	Cross-reference derived transitively from a UniProt record	UniProt-derived cross-reference	0	\N
673	Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with <em>blastx</em>.	RefSeq transcripts	0	\N
672	Cross references to RefSeq peptide sequences, determined by alignment against the proteome with <em>blastp</em>.	RefSeq peptides	0	\N
671	Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with <em>blastp</em>.	UniProt reviewed proteins	0	\N
674	Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with <em>blastp</em>.	UniProt unreviewed proteins	0	\N