Anoctamin 1 (encoded by the Ano1 gene) is a Ca2+-activated Cl- channel critical to many physiological functions. It has been speculated that Ano1 expression is regulated in a tissue-dependent manner via alternative promoters. However, variation in the 5'-end sequence of mouse Ano1 (mAno1) and its tissue-dependent regulation are poorly understood. We identified a novel 5'-terminal exon (designated exon la) of mAno1 instead of the known 5'-terminal exon (exon 0) using 5'-rapid amplification of cDNA ends (RACE) analysis. Unexpectedly, the novel 5'-end variant mAno1(Ex1a) was abundantly expressed in many tissues including the salivary and mammary glands, rectum, lung, trachea and prostate. In contrast, the known variant mAno1(EX0) predominated only in male reproductive tissues such as the epididymis and testis. In a heterologous expression system, mAno1(EX0) encoded a longer protein than mAno1(Ex1a), and this long isoform was abolished by a mutation in the exon 0 start codon. Moreover, the mAno1(EX0)-specific N-terminal sequence was immunohistochemically detected in epididymis but not in salivary gland. Our data suggest that mAno1 expression is regulated via alternative promoters, and its transcriptional variation results in variation of the N-terminal sequence of the Ano1 protein due to the alternative translation initiation sites. These tissue-specific variations might contribute to the regulation of mAno1 expression and activity according to the physiological function of each tissue. (C) 2018 Elsevier Inc. All rights reserved.