Our previous studies have demonstrated that, in addition to the conventional mu- and m-calpains ubiquitously expressed in tissues, a muscle-specific calpain comprising a novel member of the large subunit family (p94 or nCL-1, which stands for novel Calpain Large subunit) exists in muscle cells. To clarify the physiological function of nCL-1, we screened cDNA libraries of various rat tissues for other tissue-specific calpains and, as a result, discovered a novel member of the calpain large subunit family. RNA blot analysis showed that the mRNA is expressed predominantly in the stomach. Isolated cDNA clones could be structurally divided into two groups, whose 5'-halves of about 1.1 kilobase pairs were identical, but whose 3'-halves bore no similarity at all. This suggests generation by an alternative splicing mechanism, which was proved by genomic DNA cloning. Open reading frames were found encoding 703 and 381 amino acid residues with calculated molecular masses of 79,554 and 42,591 for nCL-2 and -2', respectively. The deduced amino acid sequence of nCL-2 is very similar to those of other calpain large subunits and can be aligned without significant insertions or deletions, suggesting that nCL-2 should possess cysteine protease activity and calcium binding ability. nCL-2' is identical to the N-terminal half of nCL-2 and, thus, contains only the cysteine protease domain but not the calcium binding domain. Possible roles of the calpain family are discussed based on these findings.