The definitive nonhuman primate MHC allele databases are maintained by IPD-MHC-NHP. For investigators in characterizing MHC alleles, we provide protocols and useful oligonucleotide sequences. Some of the most commonly requested MHC sequences are linked below:

Rhesus macaque (Mamu)
Mamu-A
Mamu-B
Mamu-DPA
Mamu-DPB
Mamu-DQA
Mamu-DQB
Mamu-DRA
Mamu-DRB
Mamu-E
Mamu-F
Mamu-G
Mamu-I
Mamu-AG
Cynomolgus macaque (Mafa)
Mafa-A
Mafa-B
Mafa-DPA
Mafa-DPB
<Mafa-DQA
Mafa-DQB
Mafa-DRA
Mafa-DRB
Mafa-E Mafa-G
Mafa-I
Mafa-AG
Pig-tailed macaque (Mane)
Mane-A
Mane-B
Mane-DQB
Mane-DRB
Mane-E
Mane-I
Mane-AG

FASTA files of MHC sequences can be downloaded from the IPD-MHC-NHP FTP site. Note that provisional, newer sequences that are not incorporated in the official release are found in the updates folder.

Official nomenclature of nonhuman primate MHC alleles follows the conventions established for human HLA sequences; additional information for each element of an allele name:

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Comments on nonhuman primate MHC allele databases


Rhesus macaques


The primary populations of rhesus macaques used in research come from India and China. Exports of Indian rhesus macaques were stopped in the 1970s, so the populations of Indian-origin rhesus macaques available for domestic research descend from animals that have been in the United States for several decades. Breeding colonies of rhesus macaques are supported at each National Primate Research Center. Despite the constrained supply, Indian-origin rhesus macaques remain popular among researchers. Multi-generational pedigrees are available from several breeding colonies, there is extensive historical data from Indian-origin rhesus macaques, and some investigators are reluctant to migrate projects that were started with Indian-origin rhesus macaques to other populations.

Significant numbers of Chinese rhesus macaques are imported to the United States for research. There are also large research programs using Chinese-origin rhesus macaques in Asia. The supply of Chinese-origin rhesus macaques is generally less constrained than Indian-origin rhesus macaques.

Key features of MHC allele databases in rhesus macaques:

  • Rhesus macaque MHC alleles are prefixed with 'Mamu-' (an abbreviation for their scientific name Macaca mulatta)
  • Indian-origin rhesus macaques have the most complete databases of MHC class I and class II alleles
  • We do not believe there are many additional MHC lineages in domestic Indian-origin rhesus macaques, though we expect that many new alleles within these lineages remain undiscovered
  • Since few rhesus macaques from different locations in India have had their MHC sequenced, we do not know how well existing allele databases represent true diversity in the free-living macaque population
  • There are far more MHC alleles in Chinese-origin rhesus macaques than in the domestic Indian-origin rhesus macaques. We anticipate that additional sequencing will uncover new lineages and many new alleles

Cynomolgus macaques


Cynomolgus macaques are distributed throughout southeast Asia. Additionally, an isolated population of cynomolgus macaques was introduced to the Indian Ocean island of Mauritius within the last 500 years. Macaques from all of these populations are used in domestic biomedical research. Compared to the Asian populations, Mauritian macaques have dramatically reduced MHC variation. All of the MHC class I and class II sequences in Mauritian macaques have been determined. MHC alleles in different Asian cynomolgus macaque populations (The Philippines, Indonesia, Vietnam, Laos, plus animals sold by commercial suppliers in China) overlap, but are present in different frequencies. Consequently, targeted sequencing from different populations of animals is necessary to fully populate cynomolgus macaque databases.

Key features of MHC allele databases in cynomolgus macaques:

  • Cynomolgus macaque MHC alleles are prefixed with 'Mafa-' (an abbreviation for their scientific name Macaca fascicularis)
  • Additional sequencing will likely identify new MHC lineages and a large number of new alleles
  • Even though there are roughly equal numbers of rhesus and cynomolgus macaque MHC alleles in IPD, we anticipate there are more novel alleles remaining to be discovered in cynomolgus macaques

Pig-tailed macaques


Pig-tailed macaques are larger than cynomolgus or rhesus macaques and are particularly valuable for certain research questions in transplantation and infectious disease. Comparatively small numbers of pig-tailed macaques are used for research in the United States. Consequently, MHC allele discovery is not as advanced in this population. Nonetheless, hundreds of MHC sequences have been cataloged in the last several years. Though pig-tailed macaques have a large geographic range in the wild, most of the animals used for research are thought to originate from Indonesia.

Key features of MHC allele databases in pig-tailed macaques:

  • Pig-tailed macaque MHC alleles are prefixed with 'Mane-' (an abbreviation for their scientific name Macaca nemestrina)
  • Nearly all MHC allele discovery efforts in pig-tailed macaques have occurred since 2010