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Members of the recently discovered chloride channels, calcium-activated (CLCA) gene family are thought to contribute to transmembrane trafficking of anions and other cellular functions. Previous northern blot and in situ hybridization studies revealed expression of the murine putative chloride channel mCLCA1 (alias mCaCC) in numerous epithelia and few other cell types. However, the subsequent cloning of mCLCA2 which shares 96% cDNA sequence identity with mCLCA1 suggested that the distribution pattern proposed for mCLCA1 in fact represented the sum of both mRNA species. In this study, a real-time RT-quantitative PCR assay was established to specifically quantify mCLCA1 and mCLCA2 expression in 19 pre- and 44 postnatal murine tissues. Different expression levels of mCLCA1 and mCLCA2 were found in most tissues analyzed. Particularly strong and virtually exclusive expression was found for mCLCA1 in spleen and bone marrow and for mCLCA2 in lactating and involuting mammary glands. In contrast, other tissues including intestine and trachea were found to express equally moderate levels of both homologues. Moreover, mCLCA2, but not mCLCA1, seems to be involved in stage-specific organogenesis in fetal tissues. These results indicate that, in spite of their extremely close sequence homology, mCLCA1 and mCLCA2 are involved in different, yet unidentified pathways.