10 AGI Repeat sequences repeats-AGI 1 \N 709 Conserved Domain Database models. CDD 1 {"type": "domain"} 453 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"} 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 455 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 5 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"} 710 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 729 \N GOA annotation 0 \N 490 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 244 The Gene Ontology XRef projection pipeline GO projected xrefs 0 \N 496 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 714 HAMAP families. HAMAP 1 {"type": "domain"} 718 PANTHER families. PANTHER 1 {"type": "domain"} 727 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 725 InterPro2Pathway mapping from InterproScan results. InterPro2Pathway 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 461 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"} 720 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 726 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"} 12 Genomic alignments of rice (Oryza) "Expressed Sequence Tags" (ESTs) from dbEST Rice EST 1 {"gene": {"do_not_display": "1"}, "type": "est"} 13 Genomic alignments of rice (Oryza) EST clusters (Unigenes, Gene Indices) Rice ESTCluster 1 {"type": "cdna"} 14 Genomic alignments of rice (Oryza) mRNA Rice mRNA 1 {"type": "cdna"} 15 Genomic alignments of rice (Oryza) "restriction fragment length polymorphism" (RFLP) Rice RFLP 1 {"type": "cdna"} 18 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 711 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 712 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 713 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 719 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 35 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 7 Repeats detected using the AGI library (agi_aor_v7.fa) using RepeatMasker. Repeats AGI library 1 \N 457 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 458 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 462 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"} 715 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 724 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 716 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 36 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 721 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 717 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 337 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 723 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 722 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 728 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 456 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 454 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 463 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"} 487 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 488 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 489 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 493 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 492 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 491 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 494 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N