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Proteomes - Sus scrofa (Pig)

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> 49,791
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>UP000008227
Taxonomy9823 - Sus scrofa
StrainDuroc
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000003025.6 from Ensembl 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:95.7%[S:37.8%,D:57.8%],F:0.7%,M:3.6%,n:13335 cetartiodactyla_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)

Sus scrofa, the domestic pig, is a member of the Artiodactyla (even-toed ungulates). First domesticated around 10,000 years ago, they are an important agricultural species worldwide. In addition, pigs are useful as a non-primate biomedical model organism, especially for the study of complex traits (e.g. obesity, cardiovascular disease, and arthritis) and for xenotransplantation experiments.

The first draft genome was released in 2012 by the Swine Genome Sequencing Consortium, using sequence derived from a single Duroc sow (Duroc 2-14). Assembly 10.2 contains approximately 2.6 Gb of sequence and 21,000 protein-coding genes.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome 1
CM000812
4187
Chromosome 2
CM000813
4389
Chromosome 3
CM000814
3140
Chromosome 4
CM000815
2686
Chromosome 5
CM000816
2526
Chromosome 6
CM000817
4762
Chromosome 7
CM000818
2988
Chromosome 8
CM000819
1762
Chromosome 9
CM000820
2726
Chromosome 10
CM000821
1107
Chromosome 11
CM000822
877
Chromosome 12
CM000823
2579
Chromosome 13
CM000824
3379
Chromosome 14
CM000825
3059
Chromosome 15
CM000826
2076
Chromosome 16
CM000827
880
Chromosome 17
CM000828
1428
Chromosome 18
CM000829
1110
Chromosome X
CM000830
1762
Mitochondrion
AF034253
16
Unplaced
2478
Chromosome Y
LT634572
125

Publications

  1. "Complete nucleotide sequence of pig (Sus scrofa) mitochondrial genome and dating evolutionary divergence within artiodactyla."
    Lin C.S., Sun Y.L., Liu C.Y., Yang P.C., Chang L.C., Cheng I.C., Mao S.J.T., Huang M.C.
    Gene 236:107-114(1999) [PubMed] [Europe PMC] [Abstract]
  2. Datahose
    Submitted (FEB-2017) to the EMBL/GenBank/DDBJ databases
  3. Porcine genome sequencing project
    Submitted (NOV-2009) to the EMBL/GenBank/DDBJ databases
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