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Proteomes - Arabidopsis lyrata subsp. lyrata (Lyre-leaved rock-cress)

Overview

StatusReference proteome
Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome%5Fredundancy">more...</a>)</p> 32,113
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000008694
Taxonomy81972 - Arabidopsis lyrata subsp. lyrata
Straincv. MN47
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000004255.1 from ENA/EMBL full
Buscoi <p>The Benchmarking Universal Single-Copy Ortholog (BUSCO) assessment tool is used, for eukaryotic and bacterial proteomes, to provide quantitative measures of UniProt proteome data completeness in terms of expected gene content. BUSCO scores include percentages of complete (C) single-copy (S) genes, complete (C) duplicated (D) genes, fragmented (F) and missing (M) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment, and the name of the taxonomic lineage dataset used.</p> C:95.9%[S:94.3%,D:1.6%],F:0.5%,M:3.5%,n:4596 brassicales_odb10
Completenessi <p>Complete Proteome Detector (CPD) is an algorithm which employs statistical evaluation of the completeness and quality of proteomes in UniProt, by looking at the sizes of taxonomically close proteomes. Possible values are 'Standard', 'Close to Standard' and 'Outlier'.</p> Outlier (low value)

The Brassicaceae Arabidopsis lyrata subsp. lyrata is a close relative of the model organism Arabidopsis thaliana, from which is diverged around 10 million years ago. A. lyrata is an outcrossing diploid and, unlike the (generally) self-fertilising A. thaliana, has stable and spatially restricted populations or subspecies. This means that comparisons between the genomes of the closely related species could reveal the genetic basis of the invasive spread of A. thaliana and would also provide valuable data on the evolution of the A. thaliana genome.

The genome of A. lyrata subsp. lyrata is around 50% larger than A. thaliana (207 Mb and 125 Mb respectively) and is predicted to contain more protein coding genes (32,670 genes compared to 27,025 genes in A. thaliana). Analysis of their genomes suggest that reduction in genome size is the result of large-scale rearrangements and hundreds of thousands of small deletions found throughout the genome.

Componentsi <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationProteins
Unassembled WGS sequence
ADBK01000000
32113
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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