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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> 53,336
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>UP000006729
Taxonomy3694 - Populus trichocarpa
Straincv. Nisqually
Last modifiedMarch 7, 2021
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000002775.3 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 (F) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment.</p> C:97.3%[S:50.8%,D:46.5%],F:1.2%,M:1.5%,n:2326 eudicots_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> Close to standard (high value)

Populus trichocarpa (Black cottonwood) is a fast growing deciduous tree belonging to the willow family (Salicaceae) which is grown for its timber and for fiber products, mainly in North America.

The genus Populus is widely distributed over the northern hemisphere with many species that are economically important. Populus trichocarpa was chosen as the first tree to be sequenced because of the relatively small size of its genome.

The Populus trichocarpa genome has a haploid chromosome number of 19, and with over 400 Mb is nearly four times larger than the genome of Arabidopsis. There are 44,000 protein-coding genes. About 8,000 pairs of duplicated genes are present due to an early genome duplication event.

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

Component nameGenome Accession(s)
Component representationProteins
Chloroplast88
Chromosome 71924
Chromosome 171997
Chromosome 16022
Chromosome 142562
Chromosome 121934
Chromosome 191671
Chromosome 53403
Chromosome 92145
Chromosome 103373
Chromosome 151887
Chromosome 43008
Chromosome 112162
Chromosome 181961
Chromosome 82996
Chromosome 32998
Chromosome 161832
Chromosome 63671
Chromosome 132032
Chromosome 23458
Unassembled WGS sequence2348
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Main funding by: National Institutes of Health

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