735 Conserved Domain Database models. CDD 1 {"type": "domain"} 534 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"} 83 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 708 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 757 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 3 Gene models predicted using GLEAN.Information provided by BRAD. 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"} 761 \N GOA annotation 0 \N 571 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 323 The Gene Ontology XRef projection pipeline GO projected xrefs 0 \N 712 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 737 HAMAP families. HAMAP 1 {"type": "domain"} 734 PANTHER families. PANTHER 1 {"type": "domain"} 756 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 117 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 19 zBr1005_rap_DNA_v3 from AlignStore Markers 1 {"default": {"contigviewbottom": "normal"}, "type": "marker"} 533 MicroRNA from miRBase. miRBase miRNA 1 {"type": "rna"} 542 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"} 746 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 747 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 84 Density of 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.) Non-coding genes (density) 1 \N 28 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 27 Percentage of G/C bases in the sequence. GC content 1 \N 738 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 758 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 740 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 741 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 85 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 137 InDel markers for Brassica rapa based on whole-genome re-sequencing RCZ16_DH 1 \N 711 Repeats detected using RepeatMasker to scan non-redundant elements from several plant libraries , including REdat, TREP and RepetDB among others. Repeats: nrplants 1 \N 538 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 710 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 521 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"} 755 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 751 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 743 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 116 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 749 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 750 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 82 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 744 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 745 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 748 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 709 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 535 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 544 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"} 568 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 75 Sequences from various databases are matched to Ensembl transcripts using Exonerate. These are external references, or 'Xrefs'. DNA match 0 \N 76 match Protein 0 \N 569 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 570 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 574 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 573 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 572 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 575 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N