294 Conserved Domain Database models. CDD 1 {"type": "domain"} 72 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"} 13 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 74 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 Assembly gap feature annotated in ENA Assembly gap (ENA) 1 \N 4 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"} 133 External links from plants collaborators External Plant Links 1 \N 318 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 118 Genes imported from the community GFF3. See the species 'About' page for more information. 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"} 3 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 321 \N GOA annotation 0 \N 291 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 116 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 296 HAMAP families. HAMAP 1 {"type": "domain"} 297 PANTHER families. PANTHER 1 {"type": "domain"} 316 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 53 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 80 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"} 307 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 308 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 55 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 5 Percentage of G/C bases in the sequence. GC content 1 \N 298 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 315 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 300 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 301 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 9 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 76 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 77 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 81 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"} 317 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 311 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 303 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 54 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 309 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 304 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 305 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 306 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 310 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 75 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 73 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 82 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"} 288 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 289 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 290 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 113 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 112 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 292 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 293 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N