742 Conserved Domain Database models. CDD 1 {"type": "domain"} 485 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"} 38 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 487 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 764 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 769 \N GOA annotation 0 \N 521 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 276 The Gene Ontology XRef projection pipeline GO projected xrefs 0 \N 720 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 743 HAMAP families. HAMAP 1 {"type": "domain"} 748 PANTHER families. PANTHER 1 {"type": "domain"} 765 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 76 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 370 MicroRNA from miRBase. miRBase miRNA 1 {"type": "rna"} 493 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"} 759 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 755 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 36 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 31 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 4 Percentage of G/C bases in the sequence. GC content 1 \N 745 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 766 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 1 Gene annotation by The Potato Genome Sequencing Consortium (PGSC) 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 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 747 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 37 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 489 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 490 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 494 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"} 763 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 757 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 750 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 75 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 760 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 751 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 39 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 753 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 754 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 756 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 488 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 486 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 495 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"} 519 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 33 Sequences from various databases are matched to Ensembl transcripts using Exonerate. These are external references, or 'Xrefs'. DNA match 0 \N 34 match Protein 0 \N 520 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 522 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 525 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 524 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 523 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 526 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N