9	AGI Repeat sequences	repeats-AGI	1	\N
735	<a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml">Conserved Domain Database</a> models.	CDD	1	{"type": "domain"}
479	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"}
37	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
481	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"}
756	<a href="http://www.cathdb.info/">CATH/Gene3D</a> families.	Gene3D	1	{"type": "domain"}
2	Gene annotation by <a href="http://www.omap.org/index.html">The Oryza Genome Evolution Project (OGE), previously known as OMAP</a>	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"}
762	\N	GOA annotation	0	\N
516	GO term derived transitively from a UniProt record	UniProt-derived GO term	0	\N
274	The Gene Ontology XRef projection pipeline	GO projected xrefs	0	\N
522	Gene encoding an enzyme annotated at the <a rel="external" href="https://plantreactome.gramene.org">Plant Reactome</a>.	Plant Reactome	1	\N
740	<a href="http://hamap.expasy.org/">HAMAP</a> families.	HAMAP	1	{"type": "domain"}
738	<a href="http://www.pantherdb.org/">PANTHER</a> families.	PANTHER	1	{"type": "domain"}
758	InterPro2GO mapping, defined by InterPro.	InterPro2GO mapping	0	\N
74	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
487	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"}
747	Intrinsically disordered regions predicted by <a href="http://protein.bio.unipd.it/mobidblite/">MobiDB lite</a>.	MobiDB lite	1	{"type": "feature"}
752	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"}
39	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
36	Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.)	Repeats (percent)	1	\N
38	Percentage of G/C bases in the sequence.	GC content	1	\N
737	Protein domains and motifs from the <a rel="external" href="http://pfam.xfam.org">Pfam</a> database.	Pfam	1	{"type": "domain"}
757	Protein domains and motifs from the <a rel="external" href="http://prosite.expasy.org">PROSITE</a> profiles database.	PROSITE profiles	1	{"type": "domain"}
739	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"}
744	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"}
40	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
4	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
483	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
484	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
488	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"}
759	Protein domains and motifs from the <a rel="external" href="http://prosite.expasy.org">PROSITE</a> patterns database.	PROSITE patterns	1	{"type": "domain"}
753	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"}
743	<a href="http://sfld.rbvi.ucsf.edu/">Structure-Function Linkage Database</a> families.	SFLD	1	{"type": "domain"}
73	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
750	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"}
746	Protein domains and motifs from the <a rel="external" href="http://smart.embl-heidelberg.de">SMART</a> database.	SMART	1	{"type": "domain"}
35	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
745	Protein domains and motifs from the <a rel="external" href="http://supfam.org/SUPERFAMILY">SUPERFAMILY</a> database.	Superfamily	1	{"type": "domain"}
748	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"}
749	Transmembrane helices predicted by <a rel="external" href="http://www.cbs.dtu.dk/~krogh/TMHMM">TMHMM</a>.	Transmembrane helices	1	{"type": "feature"}
482	<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
480	tRNA models predicted with <a href="http://lowelab.ucsc.edu/tRNAscan-SE">tRNAscan-SE</a> (release 1.3.1).	tRNA Models	1	{"type": "rna"}
489	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"}
513	UniParc mapping based on sequence checksums	UniParc cross-reference	0	\N
32	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
33	match	Protein	0	\N
514	UniProt cross-reference derived transitively from a UniParc identifier	UniParc-derived cross-reference	0	\N
515	Cross-reference derived transitively from a UniProt record	UniProt-derived cross-reference	0	\N
519	Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with <em>blastx</em>.	RefSeq transcripts	0	\N
518	Cross references to RefSeq peptide sequences, determined by alignment against the proteome with <em>blastp</em>.	RefSeq peptides	0	\N
517	Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with <em>blastp</em>.	UniProt reviewed proteins	0	\N
520	Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with <em>blastp</em>.	UniProt unreviewed proteins	0	\N