The nucleotide sequence and comparative analysis of the H-2D(p) class I H-2 gene

We present the complete nucleotide sequence and the deduced amino acid sequence of the H-2D(p) class I gene. This gene, which was cloned from a B10.P genomic DNA library, encodes an intact, functional H-2D(p) molecule. Comparative analysis of the D(p) sequence with other class I sequences reveals both similarities and differences. This analysis also shows that these genes exhibit D region-specific, locus-specific, as well as allele-specific sequences. The H-2D(p) nucleotide sequence is greater than 90% homologous to the H-2L(d) and H-2D^b genes and only approximately 85% homologous to the H-2D(d) gene. The K region and Qa region genes are less homologous. The 3' noncoding sequences appear to be region-specific. All of the previously described D region genes, D^b, L(d), and D(d), possess the B2-SINE Alu-like repetitive sequences, as does D(p). Thus, this B2 repeat is a region-specific marker present in all D region genes studied so far. The additional poly-adenylation site found in the H-2D(p) gene starting at nucleotide 4671, which is homologous to non-D region sequences, as well as unique protein D(p) coding sequences, make this gene an interesting model for studying the evolution of polymorphism and structure/function relationships in the class I gene family.