13 AGI Repeat sequences repeats-AGI 1 \N 705 Conserved Domain Database models. CDD 1 {"type": "domain"} 448 Covariance models from Rfam (release 12.2), aligned to the genome with 'cmscan' from the Infernal suite of programs. Models are restricted to those observed in species that share a last common ancestor (LCA). Rfam Models (LCA) 1 {"type": "rna"} 18 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 450 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 4 Ab initio prediction of protein coding genes, based on the genomic sequence alone AA Salamov et al., Genome Res. 2000 4:516-22. 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"} 725 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 731 \N GOA annotation 0 \N 485 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 243 The Gene Ontology XRef projection pipeline GO projected xrefs 0 \N 491 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 707 HAMAP families. HAMAP 1 {"type": "domain"} 709 PANTHER families. PANTHER 1 {"type": "domain"} 728 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 65 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 456 RNA genes imported from miRBase . 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"} 714 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 718 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 1 Gene annotation by Oryza Genome Evolution project (OGE) through MAKER gene annotation pipeline. Genes 1 {"caption": "OGE MAKER annotation", "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": "OGE MAKER annotation", "name": "OGE MAKER annotation"} 9 Genomic alignments of rice (Oryza) "Expressed Sequence Tags" (ESTs) from dbEST Rice EST 1 {"gene": {"do_not_display": "1"}, "type": "est"} 10 Genomic alignments of rice (Oryza) EST clusters (Unigenes, Gene Indices) Rice ESTCluster 1 {"type": "cdna"} 11 Genomic alignments of rice (Oryza) mRNA Rice mRNA 1 {"type": "cdna"} 12 Genomic alignments of rice (Oryza) "restriction fragment length polymorphism" (RFLP) Rice RFLP 1 {"type": "cdna"} 16 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 17 Percentage of G/C bases in the sequence. GC content 1 \N 706 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 726 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 711 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 712 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 20 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 6 Repeats detected using the AGI library (agi_aor_v7.fa) using RepeatMasker. Repeats AGI library 1 \N 452 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 453 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 457 RNA genes produced by filtering alignments of Rfam (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"} 727 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 719 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 713 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 19 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 720 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 715 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 717 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 716 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 723 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 451 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 449 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 458 RNA genes produced by filtering predictions from tRNAscan-SE 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"} 482 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 39 Sequences from various databases are matched to Ensembl transcripts using Exonerate. These are external references, or 'Xrefs'. DNA match 0 \N 40 match Protein 0 \N 483 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 484 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 488 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 487 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 486 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 489 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N