631	<a href="https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml">Conserved Domain Database</a> models.	CDD	1	{"type": "domain"}
458	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"}
73	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
559	Chloroplast protein-coding genes imported from <a rel="external" href="http://www.ncbi.nlm.nih.gov/genbank/">Genbank</a>.	Pt genes (GenBank)	1	{"caption": "Genes (Ensembl)", "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": "Ensembl genes"}
605	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
355	Protein coding genes annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</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"}
365	exon feature annotated in ENA	exon (ENA)	1	{"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"}
364	intron feature annotated in ENA	intron (ENA)	1	{"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"}
360	misc_feature feature annotated in ENA	misc_feature (ENA)	1	{"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"}
363	mRNA feature annotated in ENA	mRNA (ENA)	1	{"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"}
362	Repeat regions annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a>	Repeats (ENA)	1	\N
133	External links from plants collaborators	External Plant  Links	1	\N
11	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"}
653	<a href="http://www.cathdb.info/">CATH/Gene3D</a> families.	Gene3D	1	{"type": "domain"}
80	TE-related Gene annotation by <a href="http://rice.plantbiology.msu.edu">MSU</a> through a process of automatic and manual curation	TE-related Gene (MSU)	1	{"caption": "MSU7 TE-related genes", "colour_key": "[biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "label_key": "[biotype]", "multi_name": "MSU7 TE-related genes", "name": "MSU7 TE-related genes"}
357	Cross-references attached by GenomeLoader to provide names	GenomeLoader name cross-references	0	\N
356	Cross-references attached by GenomeLoader	GenomeLoader cross-references	0	\N
658	\N	GOA annotation	0	\N
535	GO term derived transitively from a UniProt record	UniProt-derived GO term	0	\N
358	ncRNA genes annotated in <a href="http://www.ebi.ac.uk/ena/">ENA</a>	ncRNA genes (ENA)	1	{"caption": "Genes", "colour_key": "[biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "ena_ncrna", "label_key": "[biotype]", "name": "ncRNA Genes"}
609	Gene encoding an enzyme annotated at the <a rel="external" href="https://plantreactome.gramene.org">Plant Reactome</a>.	Plant Reactome	1	\N
467	RNA genes produced by filtering alignments of <a href='http://rfam.xfam.org'>Rfam</a> (release 12.2) covariance models.	RNA genes	1	{"caption": "Genes", "colour_key": "[biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "rfam", "label_key": "[biotype]", "name": "Rfam RNA Genes"}
468	RNA genes produced by filtering predictions from <a href='http://lowelab.ucsc.edu/tRNAscan-SE/'>tRNAscan-SE</a> v1.23.	RNA genes	1	{"caption": "Genes", "colour_key": "[biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "trnascan", "label_key": "[biotype]", "name": "tRNA Genes"}
634	<a href="http://hamap.expasy.org/">HAMAP</a> families.	HAMAP	1	{"type": "domain"}
633	<a href="http://www.pantherdb.org/">PANTHER</a> families.	PANTHER	1	{"type": "domain"}
655	InterPro2GO mapping, defined by InterPro.	InterPro2GO mapping	0	\N
79	Gene annotation by <a href="http://rapdb.dna.affrc.go.jp/">The Rice Annotation Project (RAP)</a> dated 2017-08-04. <a href="http://plants.ensembl.org/Oryza_sativa/Info/Annotation/#genebuild">Read more...</a>	Genes (IRGSP)	1	{"caption": "IRGSP 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": "IRGSP Genes", "name": "IRGSP Genes"}
76	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
466	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"}
643	Intrinsically disordered regions predicted by <a href="http://protein.bio.unipd.it/mobidblite/">MobiDB lite</a>.	MobiDB lite	1	{"type": "feature"}
560	Mitochondrial gene models imported from <a rel="external" href="http://www.ncbi.nlm.nih.gov/genbank/">Genbank</a>.	MT genes (GenBank)	1	{"caption": "Genes (Ensembl)", "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": "Ensembl genes"}
644	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"}
72	Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.)	Repeats (percent)	1	\N
78	Percentage of G/C bases in the sequence.	GC content	1	\N
636	Protein domains and motifs from the <a rel="external" href="http://pfam.xfam.org">Pfam</a> database.	Pfam	1	{"type": "domain"}
652	Protein domains and motifs from the <a rel="external" href="http://prosite.expasy.org">PROSITE</a> profiles database.	PROSITE profiles	1	{"type": "domain"}
639	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"}
637	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"}
77	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
531	Genes by <a href="http://rapdb.dna.affrc.go.jp/">The Rice Annotation Project (RAP)</a> dated 2018-11-26.	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"}
8	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
604	Repeats detected using <a rel="external" href="http://www.repeatmasker.org">RepeatMasker</a> to scan non-redundant elements from several plant libraries , including <a href="http://mips.helmholtz-muenchen.de/plant/recat/">REdat</a>, <a href="http://botserv2.uzh.ch/kelldata/trep-db">TREP</a> and <a href="http://urgi.versailles.inra.fr/repetdb/begin.do">RepetDB</a> among others.	Repeats: nrplants	1	\N
462	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
603	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
654	Protein domains and motifs from the <a rel="external" href="http://prosite.expasy.org">PROSITE</a> patterns database.	PROSITE patterns	1	{"type": "domain"}
647	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"}
640	<a href="http://sfld.rbvi.ucsf.edu/">Structure-Function Linkage Database</a> families.	SFLD	1	{"type": "domain"}
75	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
646	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"}
641	Protein domains and motifs from the <a rel="external" href="http://smart.embl-heidelberg.de">SMART</a> database.	SMART	1	{"type": "domain"}
74	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
642	Protein domains and motifs from the <a rel="external" href="http://supfam.org/SUPERFAMILY">SUPERFAMILY</a> database.	Superfamily	1	{"type": "domain"}
645	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"}
648	Transmembrane helices predicted by <a rel="external" href="http://www.cbs.dtu.dk/~krogh/TMHMM">TMHMM</a>.	Transmembrane helices	1	{"type": "feature"}
606	<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
459	tRNA models predicted with <a href="http://lowelab.ucsc.edu/tRNAscan-SE">tRNAscan-SE</a> (release 1.3.1).	tRNA Models	1	{"type": "rna"}
532	UniParc mapping based on sequence checksums	UniParc cross-reference	0	\N
68	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
69	match	Protein	0	\N
533	UniProt cross-reference derived transitively from a UniParc identifier	UniParc-derived cross-reference	0	\N
534	Cross-reference derived transitively from a UniProt record	UniProt-derived cross-reference	0	\N
498	Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with <em>blastx</em>.	RefSeq transcripts	0	\N
497	Cross references to RefSeq peptide sequences, determined by alignment against the proteome with <em>blastp</em>.	RefSeq peptides	0	\N
536	Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with <em>blastp</em>.	UniProt reviewed proteins	0	\N
499	Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with <em>blastp</em>.	UniProt unreviewed proteins	0	\N