We isolated and analyzed a new rat gene which is homologous to the recently described human major histocompatibility complex class I-related gene MR1. The deduced amino acid sequence of the rat Mr1 gene shows conserved cysteine residues typical of class I genes as well as conserved beta2-microglobulin and CD8 contact sites. Analysis of partial DNA sequences and restriction fragment length polymorphism patterns of several inbred rat strains indicate that Mr1 is not polymorphic. Mr1 is a single-copy gene, which could be mapped to rat chromosome 13 by co-segregation analysis of Mr1 and a microsatellite marker in the renin (Ren) gene in double-backcross hybrids. The recombination frequency between both genes was determined to be 14.7% (4.9-31.1, 95% confidence limits). Expression analysis revealed various Mr1 transcripts in each organ tested and occurrence of alternative splicing.