148 Conserved Domain Database models. CDD 1 {"type": "domain"} 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 39 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"} 5 Assembly gap feature annotated in ENA Assembly gap (ENA) 1 \N 18 gene feature annotated in ENA gene (ENA) 1 {"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"} 3 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"} 172 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 4 Cross-references attached by GenomeLoader to provide names GenomeLoader name cross-references 0 \N 2 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 176 \N GOA annotation 0 \N 36 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 147 HAMAP families. HAMAP 1 {"type": "domain"} 152 PANTHER families. PANTHER 1 {"type": "domain"} 173 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 32 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 160 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 162 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 31 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 150 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 171 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 151 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 157 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 23 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 168 Repeats detected using Red (REPeatDetector) Repeats: Red 1 \N 42 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 41 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 170 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 164 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 154 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 25 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 161 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 155 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 159 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 158 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 163 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 40 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 33 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 34 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 35 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 37 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 38 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N