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Pig Assembly and Annotation Information

Sus scrofa


This site presents data from the manual annotation of the pig genome.

There are four regions of particular interest that have been annotated in depth:

  • MHC. The pig major histocompatibility complex (MHC), also known as the swine leukocyte antigen complex (SLA), spans a 2.4Mb region of submetacentric chromosome 7 (SSC7p1.1-q1.1). The pig MHC plays a unique role in histocompatibility and consequently SLA molecules are of interest for their potential role in xenotransplantation reactions. This region has been annotated on two assemblies:
    • chromosome 7-LW (WTSI): Twenty-three BACs from the SBAB pig genomic library, derived from a Large White boar homozygous for the H01 haplotype, provide coverage of the class I, III and II regions which comprise the MHC.
    • Sscrofa10.2: ~5Mbp of chromosome 7 on Sscrofa10.2 (24.7Mb - 29.8Mbp, clones CU311184.7 to CT737383.11).
  • Chromosome 17 region. A 9Mb region of pig chromosome 17 (58.2Mbp - 67.4Mbp) syntenic to human chromosome 20q13.13-q13.33 and mouse chromosome 2 (16.7Mbp - 17.8Mbp) has been annotated on Sscrofa10.2.
  • LRC. ~500kbp of Sscrofa10.2 chromosome 6 (53.5Mbp - 54Mbp) has been annotated due to its orthology with part of the leukocyte receptor complex (LRC) on human 19q13.4.
  • Chromsomes X-WTSI and Y-WTSI. The pig X and Y chromosomes have been fully manually annotated by the Havana team. The X chromosome consists of 938 clones, of these 912 are from Duroc and 26 from Large White X Meishan. The Y chromosome consists 543 clones, of these 536 are from Duroc and 7 from Large White X Meishan.


Manual annotation of the pig genome is being undertaken by the Havana group at the Wellcome Trust Sanger Institute.

External collaborators involved are:

  • Chromosome 6 LRC region: annotation is a collaboration with the Roslin Institute in Edinburgh
  • Chromosome 7-LW: the Class I region was sequenced by the INRA (France), Genoscope (France) and Tokai University (Japan). The Class II and III regions were sequenced by the Wellcome Trust Sanger Institute.
  • Chromosome 17: sequencing was carried out by the Wellcome Trust Sanger Institute in collaboration with Max.F.Rothschild, Department of Animal Science, Iowa State University, USA
  • Other genome wide annotation: annotation for the Immune Response Annotation Group is part of a community annotation project co-ordinated by Chris Tuggle (Iowa State University), Claire Rogel-Gaillard (INRA) and Jane Loveland (WTSI). This annotation has been perfomed under the guidance of the Havana group.


  • Renard C, Hart E, Sehra H, Beasley H, Coggill P, Howe K, Harrow J, Gilbert J, Sims S, Rogers J, Ando A, Shigenari A, Shiina T, Inoko H, Chardon P, Beck S.
    The genomic sequence and analysis of the swine major histocompatibility complex
    Genomics 2006 Volume 88, Issue 1, July 2006, Pages 96-110. [Pubmed]
  • Loveland JE, Gilbert JG, Griffiths E and Harrow JL. (2012)
    Community gene annotation in practice. Database (Oxford). 2012 Mar 20;2012:bas009. doi: 10.1093/database/bas009. Print 2012.
  • Dawson HD, Loveland JE et al (2013).
    Structural and functional annotation of the porcine immunome. BMC Genomics 2013 May 15;14:332. doi: 10.1186/1471-2164-14-332.

Genome Summary

Last Full Update 25 August 2015
Datafreeze Date 8 June 2015
Total Bases 2,919,139,706
Golden Path Length 2,595,001,740
Annotated bases 224,723,965

SScrofa10.2 assembly genes

Havana: 2,043
Protein coding 1,686
lncRNAs: 55
lincRNA 35
antisense 15
non coding 5
Unclassified processed transcripts 79
Pseudogenes: 200
processed pseudogene 163
unprocessed pseudogene 31
unitary pseudogene 3
IG pseudogene 2
pseudogene 1
IG 23

Chromosome 7-LW genes

Havana: 151
Protein coding 129
Unclassified processed transcripts 4
Pseudogenes 18

WTSI allosome genes

Havana: 1,231
Protein coding 770
lncRNAs 102
Unclassified processed transcripts 11
Pseudogenes 347
Other 1
Readthrough genes 13

About this species