64 Conserved Domain Database models. CDD 1 {"type": "domain"} 56 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 31 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"} 20 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"} 19 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"} 85 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 89 \N GOA annotation 0 \N 28 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 62 HAMAP families. HAMAP 1 {"type": "domain"} 65 PANTHER families. PANTHER 1 {"type": "domain"} 83 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 58 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 77 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 75 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 61 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 60 Percentage of G/C bases in the sequence. GC content 1 \N 67 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 86 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 68 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 69 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 57 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 34 Repeats detected using RepeatMasker to scan non-redundant elements from several plant libraries , including REdat, TREP and RepetDB among others. Repeats: nrplants 1 \N 23 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 16 Non-coding RNA gene models based on alignment by of RFAM families to genomic sequences (alignments provided by RFAM) RFAM 1 {"caption": "RFAM Genes", "colour_key": "[biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "rfam_genes", "label_key": "[biotype]", "multi_caption": "RFAM Genes", "name": "Non-coding RNA genes based on RFAM alignments"} 84 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 78 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 73 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 59 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 76 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 71 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 72 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 74 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 79 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 32 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 25 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 26 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 27 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 29 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 30 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N