506 Conserved Domain Database models. CDD 1 {"type": "domain"} 277 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"} 472 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 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"} 7 3'UTR feature annotated in ENA 3'UTR (ENA) 1 {"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"} 8 5'UTR feature annotated in ENA 5'UTR (ENA) 1 {"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"} 9 Assembly gap feature annotated in ENA Assembly gap (ENA) 1 \N 519 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 3 Cross-references attached by GenomeLoader to provide names GenomeLoader name cross-references 0 \N 2 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 524 \N GOA annotation 0 \N 313 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 475 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 497 HAMAP families. HAMAP 1 {"type": "domain"} 501 PANTHER families. PANTHER 1 {"type": "domain"} 520 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 285 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"} 510 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 512 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 499 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 521 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 502 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 508 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 471 Repeats detected using RepeatMasker to scan non-redundant elements from several plant libraries , including REdat, TREP and RepetDB among others. Repeats: nrplants 1 \N 281 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 474 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 286 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"} 518 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 511 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 504 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 514 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 505 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 507 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 509 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 513 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 473 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 278 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 287 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"} 311 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 312 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 314 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 317 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 316 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 315 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 318 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N