7 Genomic alignments of Arabidopsis "Expressed Sequence Tags" (ESTs) from dbEST EST (Arabidopsis) 1 {"gene": {"do_not_display": "1"}, "type": "est"} 2 Alignments of EST clusters (Unigenes, Gene Indices) from Arabidopsis EST Cluster (Arabidopsis) 1 {"type": "cdna"} 769 Conserved Domain Database models. CDD 1 {"type": "domain"} 502 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"} 56 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 3 Alignmments of EST clusters (Unigenes, Gene Indices) from all dicot species EST Cluster (Dicot) 1 {"type": "cdna"} 505 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 35 Ab initio prediction of protein coding genes, based on the genomic sequence alone AA Salamov et al., Genome Res. 2000 4:516-22. FGENESH prediction 1 {"caption": "FGENESH prediction", "colour_key": "[biotype]", "default": {"MultiBottom": "collapsed_label", "MultiTop": "gene_label", "alignsliceviewbottom": "as_collapsed_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label", "cytoview": "gene_label"}, "key": "fgenesh", "label_key": "[biotype]", "multi_name": "FGENESH prediction", "name": "FGENESH prediction"} 785 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 1 Gene annotation by JGI through a process of automatic and manual curation 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"} 788 \N GOA annotation 0 \N 539 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 292 The Gene Ontology XRef projection pipeline GO projected xrefs 0 \N 548 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 764 HAMAP families. HAMAP 1 {"type": "domain"} 762 PANTHER families. PANTHER 1 {"type": "domain"} 783 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 92 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 6 Alignments of EST clusters (Unigenes, Gene Indices) from Maize EST Cluster (Maize) 1 {"type": "cdna"} 504 MicroRNA from miRBase. miRBase miRNA 1 {"type": "rna"} 773 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 4 Alignments of EST clusters (Unigenes, Gene Indices) from monocot species EST Cluster (Monocot) 1 {"type": "cdna"} 774 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 57 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 14 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 13 Percentage of G/C bases in the sequence. GC content 1 \N 763 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 784 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 765 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 766 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 58 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 507 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 508 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 513 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"} 5 Alignments of EST clusters (Unigenes, Gene Indices) from rice (Oryza) species EST Cluster (Rice) 1 {"type": "cdna"} 782 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 777 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 768 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 91 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 775 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 770 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 771 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 772 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 776 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 506 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 503 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 511 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"} 537 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 28 Sequences from various databases are matched to Ensembl transcripts using Exonerate. These are external references, or 'Xrefs'. DNA match 0 \N 29 match Protein 0 \N 538 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 540 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 543 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 542 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 541 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 544 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N