542 Conserved Domain Database models. CDD 1 {"type": "domain"} 286 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"} 22 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 289 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 16 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"} 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"} 544 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 3 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 562 \N GOA annotation 0 \N 322 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 329 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 543 HAMAP families. HAMAP 1 {"type": "domain"} 556 PANTHER families. PANTHER 1 {"type": "domain"} 559 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 561 InterPro2Pathway mapping from InterproScan results. InterPro2Pathway mapping 0 \N 148 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 295 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"} 554 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 555 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 146 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 18 Percentage of G/C bases in the sequence. GC content 1 \N 545 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 546 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 552 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 547 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 147 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 291 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 288 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 296 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"} 553 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 560 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 548 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 149 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 557 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 549 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 550 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 551 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 558 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 290 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 287 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 294 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"} 320 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 125 Sequences from various databases are matched to Ensembl transcripts using Exonerate. These are external references, or 'Xrefs'. DNA match 0 \N 321 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 323 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 326 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 325 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 324 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 327 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N