The pigment cell-specific gene, located at the brown (b) locus in mouse, has been cloned and characterized. Its gene product is required for the formation of black melanin rather than brown, although its exact function remains to be elucidated. We thus tentatively named it b-locus protein in this report. The b-locus protein gene is about 18 kilobase pairs long and organized into 8 exons and 7 introns. Functional analysis of its promoter region suggests that the nucleotide residues -38/154 is sufficient to direct the pigment cell-specific transcription in melanoma whole cell extracts. On the other hand, we were unable to detect its transcripts in HeLa whole cell extracts. Sequence comparison with the promoter region of the tyrosinase gene, another pigment cell-specific gene, reveals that two elements of the b-locus protein gene (-33/-24 and 18/28) are also conserved in the tyrosinase gene at equivalent positions, suggesting that these two elements may be involved in their pigment cell-specific transcription. Furthermore, we have cloned a cDNA, pMT3, coding for an isoform of b-locus protein from a cDNA library of mouse B16 melanoma cells. Sequence analysis of pMT3 reveals a deletion of 103 base pairs, which corresponds to the 5'-end of the exon 8 of the b-locus protein gene, indicating that pMT3 represents a mRNA species generated by alternative splicing. Since this deletion changes the reading frame and eliminates the transmembrane domain of b-locus protein, the pMT3-type mRNA may code for a soluble isoform. Such an isoform, consisting of 553 amino acids, differs only in its carboxyl terminus and is larger than b-locus protein by 16 amino acids. Using transient expression assays, we confirmed that such an isoform is able to react with anti-b-locus protein monoclonal antibody, TMH-1, suggesting that a b-locus protein isoform may have some function in pigmentation.