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I've been trying to find complete sequences of mouse (Mus musculus) MHC H2 locus haplotypes for quite some time now with limited success. The EBI IMGT database has a table of mouse H2 haplotypes, yet IMGT only provides haplotype sequences for human HLA genes via an FTP sever. I've found similar data for several other species at EBI's IPD-MHC, but Mus musculus is not on the list. The MGI database provides access to H2 SNPs, but I haven't found a mapping from SNP combinations to reconstruct happlotype sequences given reference genes.

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  • $\begingroup$ Are you after amino acid or gene sequences? $\endgroup$ – David Jun 8 at 20:55
  • $\begingroup$ @David I'm looking for nucleotide sequences: "I haven't found a mapping from SNP combinations to reconstruct happlotype sequences given reference genes". Protein sequences are readily available in the UniProt database. $\endgroup$ – Eli Korvigo Jun 15 at 11:36
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I have also hit this issue. I was interested in full length amino acid sequences for the classical class I mouse MHC alleles. I was able to find a number of them on uniprot but not all. Here is my list below. Interested if anyone knows additional sequences to extend this:

H-2 D

H-2 K

H-2 L

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  • $\begingroup$ Seems a useful answer to me, but I wonder whether the poster wanted gene or protein sequences. He didn’t say. $\endgroup$ – David Jun 8 at 20:57
  • $\begingroup$ Thank you for your effort. I've been using these UniProt protein sequences myself, but the question is about nucleotide sequences. Those are harder to find. $\endgroup$ – Eli Korvigo Jun 15 at 11:37

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