Calcyon was recently identified as a D1 dopamine receptor (DR1) interacting protein. Previous studies show that calcyon can potentiate DR1 mediated intracellular Ca(2+) release in transfected HEK293 cells, and may play an important role in DR1 Ca(2+) signaling in brain. We report that similar to the genomic structure of the human gene, the mouse calcyon gene contains six relatively short exons, with a large intron (about 8.4 kb) between exons one and two. The mouse and human calcyon genes exhibit a high level of sequence homology (77.5% at the nucleotide level) within coding regions. Northern blot and RT-PCR analyses reveal that mouse calcyon transcripts are most abundant in brain, but also present in testis and ovary, as well as in kidney and heart at much lower levels. The most distal of the transcript initiation sites identified by 5' RACE is located 159 nucleotides upstream of the putative start of translation. BLAST search of the NCBI mouse EST database and RT-PCR analysis uncovered two differentially spliced transcripts, "mcal-A" and "mcal-B." The two transcripts are identical, except that mcal-B contains a longer 3' untranslated region due to retention of a short intron (I5) between exons five and six. However, mcal-A represents the predominant calcyon transcript in mouse tissue. Further, the presence of I5 produced no detectable differences in the biosynthesis of calcyon polypeptide when expressed in HEK293, MDCK and Neuro2a cells.