For human MHC (HLA) alleles there is a ftp download available for the CDS of all HLA alleles at ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/ in FASTA.
I am looking for something equivalent, but just for mice.
Any suggestions?
Thanks
This could be tough because I found SNP information for H2 gene H2-Oa for 17 different mouse strains. Thus, there are many different allele-specific CDSs for mouse. I found this information from the Jackson Lab website http://www.informatics.jax.org
Even if your interests are with just one or two strains, the Jax site may be good as it will give you the alleles for those strains and you'd be confident that the alleles are specifically for DBA/2J, e.g., and not another strain.
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Thank you for the answer. I also got help form the staff of the Jackson Lab via mail. I filtered the database by searching for "histocompatibility". But I am wondering why there is no sequence available for the alleles of a gene (e.g. Black6 mice e.g. express the haplotype b on MHCI, which is H2-Db and H2-Kb. H2-Db is an allele of the gene H2-D1. Another allele of this gene is H2-DK. I would like to have the sequences of these alleles, but all I find is the sequence for H2-D1. I know from HLA, that there is the IMGT/HLA database, which provides CDS for all alleles. Any suggestions?
When I look at http://www.ncbi.nlm.nih.gov/gene/14972 I see links to several different H2-K seqs from different strains. You could collect the coding seqs. Alternatively, build each CDS with teh SNPs displayed at the Jax site. That's about all I can tell you as these is not my areas of research: mouse strains, histocompatibility.