29 ProDom domains. ProDom 1 {"type": "domain"} 30 Conserved Domain Database models. CDD 1 {"type": "domain"} 13 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"} 54 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 15 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 31 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 50 \N GOA annotation 0 \N 20 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 32 HAMAP families. HAMAP 1 {"type": "domain"} 33 PANTHER families. PANTHER 1 {"type": "domain"} 49 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 51 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 24 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"} 42 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 43 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 56 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 52 Percentage of G/C bases in the sequence. GC content 1 \N 34 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 35 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 36 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 37 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 53 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 17 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 18 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 5 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"} 38 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 46 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 39 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 55 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 44 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 40 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 45 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 41 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 47 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 16 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 14 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 26 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"} 2 Low confidence gene annotation by WEWseq Low confidence gene annotation by WEWseq 1 {"caption": "Genes", "colour_key": "[gene.logic_name]_[gene.biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "wewseq_lc", "label_key": "[biotype]", "name": "Low confidence gene annotation by WEWseq"} 10 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 19 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 21 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 27 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 23 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 22 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 28 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N