447 Conserved Domain Database models. CDD 1 {"type": "domain"} 191 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"} 193 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 2 Protein coding genes annotated in ENA 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"} 20 Assembly gap feature annotated in ENA Assembly gap (ENA) 1 \N 1 Repeat regions annotated in ENA Repeats (ENA) 1 \N 8 ncRNA genes annotated in ENA ncRNA genes (ENA) 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"} 470 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 9 Cross-references attached by GenomeLoader to provide names GenomeLoader name cross-references 0 \N 3 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 476 \N GOA annotation 0 \N 227 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 234 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 450 HAMAP families. HAMAP 1 {"type": "domain"} 449 PANTHER families. PANTHER 1 {"type": "domain"} 473 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 199 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"} 456 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 460 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 452 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 471 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 453 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 459 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 468 Repeats detected using Red (REPeatDetector) Repeats: Red 1 \N 195 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 196 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 201 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"} 472 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 464 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 455 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 463 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 462 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 458 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 457 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 461 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 194 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 192 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 200 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"} 225 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 75 Sequences from various databases are matched to Ensembl transcripts using Exonerate. These are external references, or 'Xrefs'. DNA match 0 \N 226 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 228 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 231 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 230 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 229 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 232 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N