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MHC regions in Vega

The major histocompatibility complex (MHC) is a significant region of the genome since many genetic determinants for autoimmune diseases and some infectious diseases have been linked to it. It contains many immune related genes including highly polymorphic genes encoding MHC class I and class II molecules that present antigens to T lymphocytes. Consequently it has been a focus for manual annotation, which has been performed in a number of different human haplotypes, mouse strains, and vertebrate species.

Vega shows the annotation of these regions, and also includes comparative pairwise analyses of them. This involves comparisons within a single species, for example between different human haplotypes, and also between species. For further details on the regions used in this analysis see our comparative analysis documentation.


Annotation of eight human MHC haplotypes was originally undertaken as part of the Chromosome 6 MHC Haplotype Project. More information about that project, including links to the haplotypic regions themselves, can be found on that page.


In addition to annotation of the MHC of the C57BL/6J reference strain, the MHC region of two mouse strains (NOD/MrkTac, NOD/ShiLtJ), used as models for Insulin-Dependent Diabetes (Idd), have been annotated as part of a larger project to sequence candidate Idd susceptibility loci. In the context of that project, the MHC region is known as Idd1. For further information, including links to the regions themselves, see the mouse regions page.


The MHC region of pig (also known as SLA, the swine leukocyte antigen complex) is of further interest because of its potential role in xenotransplantation. In addition to being annotated on the main Sscrofa10.2 assembly using BACs primarily from the Duroc breed, this region has also been annotated on an assembly from the Large White breed. For further information about this region, and the pig annotation in general, see the pig assembly and annotation page.

Rat, Chimpanzee, Gorilla, Wallaby, Dog & Tasmanian Devil

Details of the MHC regions of these species, and links to annotation can be found on the relevant species' homepages.


In Zebrafish the MHCI region on chromosome 19 has been annotated.