The calcium channel alpha1E subunit was originally cloned from mammalian brain. A new splice variant was recently identified in rat islets of Langerhans and in human kidney by the polymerase chain reaction. The same isoform of alpha1E was detected in rat and guinea pig heart by amplifying indicative cDNA fragments and by immunostaining using peptide-specific antibodies. The apparent molecular size of cardiac alpha1E was determined by SDS-PAGE and immunoblotting (218 +/- 6 kD; n = 3). Compared to alpha1E from stably transfected HEK-293 cells, this is smaller by 28 kD. The distribution of alpha1E in cardiac muscle cells of the conducting system and in the cardiomyoblast cell line H9c2 was compared to the distribution of chromogranin, a marker of neuroendocrine cells, and to the distribution of atrial natriuretic peptide (ANP). In serial sections from atrial and ventricular regions of rat heart, co-localization of alpha1E with ANP was detected in atrium and with chromogranin A/B in Purkinje fibers of the conducting system in both rat atrium and ventricle. The kidney is another organ in which natriuretic peptide hormones are secreted. The detection of alpha1E in the distal tubules of human kidney, where urodilatin is stored and secreted, led to the conclusion that the expression of alpha1E in rat heart and human kidney is linked to regions with endocrine functions and therefore is involved in the Ca(2+)-dependent secretion of peptide hormones such as ANP and urodilatin.