The mouse Cig30 gene codes for a 30-kDa membrane glycoprotein, which appears to have a role in the recruitment of brown adipose tissue. To elucidate the structure of the Cig30 gene, we have isolated a lambda phage genomic DNA clone containing the entire mouse gene and found that Cig30 consists of four exons that are spread over 4 kilobase pairs of genomic sequence. Using a fluorescence in situ hybridization assay and interspecific backcross panel mapping, we have localized the Cig30 locus to the distal region of mouse chromosome 19, between the Tlx1 and Ins1 loci. Sequencing of the corresponding lambda clone to completion revealed that the insert contained yet another gene in the opposite orientation. It turned out to be the newly identified homeobox gene Pitx3. Interestingly, the genes are very tightly linked, so that the 3' ends of their transcripts are complementary. Thus, our results provide evidence for bidirectional transcription of a several hundred base pair-long DNA region as a result of the extremely tight linkage between Cig30 and Pitx3.