The role of an IgG-Fc receptor (FcRn) that resembles a class I MHC Ag in transporting IgGs through epithelial cells was recently shown in selected species. Here we report our preliminary characterization of a clone encoding the alpha chain of the bovine FcRn from a BAC library. The recombinant BAC DNA was digested, analyzed by Southern blot hybridization and a bovine FcRn positive 9 kb long fragment was subcloned and partially sequenced. The exon/intron organization of the bovine FcRn alpha chain gene was deduced by comparison with its cDNA sequence. The sequence revealed a similar organization to the human and mouse FcRn alpha chain genes. The bovine FcRn alpha chain gene has acquired several repetitive sequences in its 5'-flanking region, including multiple SINE and LINE elements. Potential binding sites for transcription factors within the 5'-flanking sequence were identified using TESS and TFSEARCH programs. The 5'-flanking region of the bFcRn alpha chain gene was analyzed for its ability to directly express the luciferase reporter gene in bovine mammary gland epithelial cells. Transient transfection of a luciferase construct revealed that there was promoter activity in the region -1787 to +92 of the 5'-flanking sequence.