527 Conserved Domain Database models. CDD 1 {"type": "domain"} 271 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"} 17 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 273 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 1 Assembly gap feature annotated in ENA Assembly gap (ENA) 1 \N 551 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 556 \N GOA annotation 0 \N 307 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 62 The Gene Ontology XRef projection pipeline GO projected xrefs 0 \N 314 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 530 HAMAP families. HAMAP 1 {"type": "domain"} 529 PANTHER families. PANTHER 1 {"type": "domain"} 553 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 14 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 279 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"} 537 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 541 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 15 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 2 Percentage of G/C bases in the sequence. GC content 1 \N 531 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 550 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 535 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 534 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 13 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 548 Repeats detected using Red (REPeatDetector) Repeats: Red 1 \N 275 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 276 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 280 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"} 552 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 546 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 533 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 16 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 542 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 538 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 540 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 8 Genes annotated by TGAC 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"} 539 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 543 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 274 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 272 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 281 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"} 305 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 83 Sequences from various databases are matched to Ensembl transcripts using Exonerate. These are external references, or 'Xrefs'. DNA match 0 \N 306 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 308 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 311 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 310 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 309 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 312 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N