Organization and structure of the Qa genes of the major histocompatibility complex of the C3H mouse: implications for Qa function and class I evolution

We have determined the structure and organization of the entire Qa family of class I genes from the major histocompatibility complex of the C3H mouse. Restriction maps of overlapping lambda and cosmid clones reveal that there are only five Qak genes: Q1k, Q2k, Q4k, Q10k and a Q5/9 hybrid, presumably generated by unequal homologous recombination. The resulting deletion of Q6‐Q9 is consistent with the Qa‐2null phenotype of this mouse strain. We have sequenced the Qak genes, and predict that each may encode a class I molecule with a structure comparable with that proposed for the transplantation antigens. Furthermore, these Qa products should be able to bind peptides and interact with appropriate T‐cell receptors. Interestingly, in comparing Qak and H‐2k sequences, we find limited evidence of interlocus gene conversion between Qa and H‐2 loci, suggesting that the Qa genes are not likely to serve as a reservoir of genetic information for the generation of H‐2 diversity within this haplotype.