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.
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: