9 AGI Repeat sequences repeats-AGI 1 \N 703 Conserved Domain Database models. CDD 1 {"type": "domain"} 446 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"} 16 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 448 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"} 723 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 729 \N GOA annotation 0 \N 482 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 241 The Gene Ontology XRef projection pipeline GO projected xrefs 0 \N 489 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 707 HAMAP families. HAMAP 1 {"type": "domain"} 704 PANTHER families. PANTHER 1 {"type": "domain"} 725 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 63 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 454 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"} 715 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"} 10 Genomic alignments of rice (Oryza) "Expressed Sequence Tags" (ESTs) from dbEST Rice EST 1 {"gene": {"do_not_display": "1"}, "type": "est"} 11 Genomic alignments of rice (Oryza) EST clusters (Unigenes, Gene Indices) Rice ESTCluster 1 {"type": "cdna"} 12 Genomic alignments of rice (Oryza) mRNA Rice mRNA 1 {"type": "cdna"} 13 Genomic alignments of rice (Oryza) "restriction fragment length polymorphism" (RFLP) Rice RFLP 1 {"type": "cdna"} 20 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 19 Percentage of G/C bases in the sequence. GC content 1 \N 711 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 724 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 706 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 710 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 17 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 450 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 451 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 455 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"} 726 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 716 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 712 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 18 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 719 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 708 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 713 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 714 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 721 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 449 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 447 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 456 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"} 480 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 481 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 483 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 486 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 485 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 484 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 487 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N