6	AGI Repeat sequences	repeats-AGI	1	\N
16	Alignments of EST clusters (Unigenes, Gene Indices) from Arabidopsis	EST Cluster (Arabidopsis)	1	{"type": "cdna"}
741	<a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml">Conserved Domain Database</a> models.	CDD	1	{"type": "domain"}
485	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"}
41	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
487	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
7	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"}
764	<a href="http://www.cathdb.info/">CATH/Gene3D</a> families.	Gene3D	1	{"type": "domain"}
768	\N	GOA annotation	0	\N
521	GO term derived transitively from a UniProt record	UniProt-derived GO term	0	\N
277	The Gene Ontology XRef projection pipeline	GO projected xrefs	0	\N
528	Gene encoding an enzyme annotated at the <a rel="external" href="https://plantreactome.gramene.org">Plant Reactome</a>.	Plant Reactome	1	\N
743	<a href="http://hamap.expasy.org/">HAMAP</a> families.	HAMAP	1	{"type": "domain"}
744	<a href="http://www.pantherdb.org/">PANTHER</a> families.	PANTHER	1	{"type": "domain"}
762	InterPro2GO mapping, defined by InterPro.	InterPro2GO mapping	0	\N
77	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
18	Alignments of EST clusters (Unigenes, Gene Indices) from Maize	EST Cluster (Maize)	1	{"type": "cdna"}
4	Oryza glaberrima genes annotated by MIPS	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"}
493	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"}
753	Intrinsically disordered regions predicted by <a href="http://protein.bio.unipd.it/mobidblite/">MobiDB lite</a>.	MobiDB lite	1	{"type": "feature"}
754	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"}
42	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
15	Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.)	Repeats (percent)	1	\N
39	Percentage of G/C bases in the sequence.	GC content	1	\N
745	Protein domains and motifs from the <a rel="external" href="http://pfam.xfam.org">Pfam</a> database.	Pfam	1	{"type": "domain"}
763	Protein domains and motifs from the <a rel="external" href="http://prosite.expasy.org">PROSITE</a> profiles database.	PROSITE profiles	1	{"type": "domain"}
747	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"}
748	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"}
43	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
9	Repeats detected using the AGI library (agi_aor_v7.fa) using <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a>.	Repeats AGI library	1	\N
489	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
490	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
494	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"}
19	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"}
17	Alignments of EST clusters (Unigenes, Gene Indices) from rice (Oryza) species	EST Cluster (Rice)	1	{"type": "cdna"}
5	Oryza glaberrima RNA genes annotated by MIPS	ncRNA	1	{"caption": "RNA Gene (MIPS)", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "ncRNA", "label_key": "[text_label] [display_label]", "multi_name": "RNA Gene (MIPS)", "name": "RNA Gene (MIPS)"}
765	Protein domains and motifs from the <a rel="external" href="http://prosite.expasy.org">PROSITE</a> patterns database.	PROSITE patterns	1	{"type": "domain"}
759	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"}
750	<a href="http://sfld.rbvi.ucsf.edu/">Structure-Function Linkage Database</a> families.	SFLD	1	{"type": "domain"}
76	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
757	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"}
751	Protein domains and motifs from the <a rel="external" href="http://smart.embl-heidelberg.de">SMART</a> database.	SMART	1	{"type": "domain"}
40	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
755	Protein domains and motifs from the <a rel="external" href="http://supfam.org/SUPERFAMILY">SUPERFAMILY</a> database.	Superfamily	1	{"type": "domain"}
752	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"}
756	Transmembrane helices predicted by <a rel="external" href="http://www.cbs.dtu.dk/~krogh/TMHMM">TMHMM</a>.	Transmembrane helices	1	{"type": "feature"}
488	<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
486	tRNA models predicted with <a href="http://lowelab.ucsc.edu/tRNAscan-SE">tRNAscan-SE</a> (release 1.3.1).	tRNA Models	1	{"type": "rna"}
495	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"}
519	UniParc mapping based on sequence checksums	UniParc cross-reference	0	\N
20	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
21	match	Protein	0	\N
520	UniProt cross-reference derived transitively from a UniParc identifier	UniParc-derived cross-reference	0	\N
522	Cross-reference derived transitively from a UniProt record	UniProt-derived cross-reference	0	\N
525	Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with <em>blastx</em>.	RefSeq transcripts	0	\N
524	Cross references to RefSeq peptide sequences, determined by alignment against the proteome with <em>blastp</em>.	RefSeq peptides	0	\N
523	Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with <em>blastp</em>.	UniProt reviewed proteins	0	\N
526	Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with <em>blastp</em>.	UniProt unreviewed proteins	0	\N