608 Conserved Domain Database models. CDD 1 {"type": "domain"} 352 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"} 354 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 3 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"} 632 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 635 \N GOA annotation 0 \N 389 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 136 The Gene Ontology XRef projection pipeline GO projected xrefs 0 \N 395 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 614 HAMAP families. HAMAP 1 {"type": "domain"} 610 PANTHER families. PANTHER 1 {"type": "domain"} 631 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 360 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"} 621 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 622 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 27 Genomic alignments of rice (Oryza) "Expressed Sequence Tags" (ESTs) from dbEST Rice EST 1 {"gene": {"do_not_display": "1"}, "type": "est"} 26 Genomic alignments of rice (Oryza) EST clusters (Unigenes, Gene Indices) Rice ESTCluster 1 {"type": "cdna"} 28 Genomic alignments of rice (Oryza) mRNA Rice mRNA 1 {"type": "cdna"} 612 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 629 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 613 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 617 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 5 Repeats detected using the AGI library (agi_aor_v7.fa) using RepeatMasker. Repeats AGI library 1 \N 356 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 357 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 361 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"} 630 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 624 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 615 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 623 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 616 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 618 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 620 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 626 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 355 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 353 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 362 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"} 386 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 387 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 388 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 392 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 391 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 390 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 393 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N