343 Conserved Domain Database models. CDD 1 {"type": "domain"} 87 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"} 27 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 89 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 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"} 18 Assembly gap feature annotated in ENA Assembly gap (ENA) 1 \N 17 mRNA feature annotated in ENA mRNA (ENA) 1 {"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"} 366 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 2 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 372 \N GOA annotation 0 \N 123 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 130 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 346 HAMAP families. HAMAP 1 {"type": "domain"} 345 PANTHER families. PANTHER 1 {"type": "domain"} 369 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 67 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 95 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"} 356 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 357 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 70 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 347 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 367 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 348 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 349 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 69 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 364 Repeats detected using Red (REPeatDetector) Repeats: Red 1 \N 91 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 92 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 96 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"} 368 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 360 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 354 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 68 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 359 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 351 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 352 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 355 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 358 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 90 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 88 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 97 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"} 121 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 122 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 124 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 127 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 126 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 125 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 128 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N