220 Conserved Domain Database models. CDD 1 {"type": "domain"} 62 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"} 14 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 66 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 133 External links from plants collaborators External Plant Links 1 \N 242 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 247 \N GOA annotation 0 \N 102 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 198 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 223 HAMAP families. HAMAP 1 {"type": "domain"} 222 PANTHER families. PANTHER 1 {"type": "domain"} 243 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 5 Genes annotated with high confidence by IWGSC Genes annotated with high confidence by IWGSC 1 {"caption": "Genes", "colour_key": "[gene.logic_name]_[gene.biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "ensembl", "label_key": "[biotype]", "name": "Genes annotated with high confidence by IWGSC"} 16 KASP markers were designed to be genome-specific with PolyMarker. For details on how to interpret the annotation and details please visit http://www.polymarker.info/about. KASP markers 0 \N 6 Long non coding RNA generated by IWGSC using GMAP Long non coding RNA 1 {"type": "rna"} 8 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 73 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"} 7 microRNAs generated by IWGSC microRNA 1 {"type": "rna"} 233 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 234 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 11 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 9 Percentage of G/C bases in the sequence. GC content 1 \N 224 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 241 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 226 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 227 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 10 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 68 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 67 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 74 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"} 244 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 237 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 229 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 12 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 235 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 230 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 13 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 231 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 109 Tallymer is used to annotate repeated sequences in plant genomes by computing K-mer frequencies. Repeats: Tallymer 1 \N 232 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 236 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 65 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 63 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 75 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"} 99 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 100 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 101 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 105 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 104 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 103 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 106 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N