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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> 27,249
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>UP000007635
Taxonomy69293 - Gasterosteus aculeatus
Last modifiedDecember 21, 2020
Genome assemblyi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> from Ensembl
Genome annotationi Ensembl
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:88.9%[S:67.3%,D:21.6%],F:4.1%,M:7%,n:3640 actinopterygii_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 (low)

Gasterosteus aculeatus, or the three-spined stickleback, is a fish native to most inland coastal waters north of 30 N. However, as they are anadromous they can also be found in freshwater during breeding times. The three-spined stickleback has long been a subject of scientific study for many reasons. It shows great morphological variation throughout its range, which is ideal for questions about evolution and population genetics. Sticklebacks have four color photoreceptor cells in their retina making them tetrachromatic (RGB + UV). The three-spined stickleback has recently become an important organism for research that looks into the genetic changes involved in adapting to new environments.

The genome of a female fish from Bear Paw Lake in Alaska was sequenced by the Broad Institute, using whole-genome shotgun sequencing with a base coverage of approximately 11x. The stickleback genome contains approximately 460 Mb and comprises 22 pairs of chromosomes. The current assembly includes 1,822 unplaced super-contigs, and is predicted to contain 20,787 protein-coding genes.

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

Component nameGenome Accession(s)
Component representationProteins
Unassembled WGS sequence27249

Publications

  1. Lindblad-Toh K., Mauceli E., Grabherr M., Chang J.L., Lander E.S.
    Submitted (JAN-2006) to the EMBL/GenBank/DDBJ databases
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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