437 Conserved Domain Database models. CDD 1 {"type": "domain"} 178 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"} 23 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 180 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"} 1 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"} 456 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 3 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 462 \N GOA annotation 0 \N 215 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 413 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 436 HAMAP families. HAMAP 1 {"type": "domain"} 439 PANTHER families. PANTHER 1 {"type": "domain"} 457 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 56 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 177 MicroRNA from miRBase. miRBase miRNA 1 {"type": "rna"} 186 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"} 448 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 446 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 59 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 438 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 458 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 441 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 442 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 55 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 182 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 183 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 187 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"} 459 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 452 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 447 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 58 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 449 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 445 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 57 Density of single nucleotide polymorphisms (SNPs), calculated by dividing the chromosome into 150 "bins" and counting the SNPs in each. (For very short chromosomes, e.g. MT, some SNPs contribute to multiple bins.) SNP Density 1 \N 444 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 453 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 450 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 181 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 179 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 188 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"} 212 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 213 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 214 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 218 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 217 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 216 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 219 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N