Inositol 1,4,5-trisphosphate receptor type 1 (IP(3)R1) is already known to be highly expressed in the brain, and is found in many other tissues, including the atrium of the heart. Although the complete primary structure of IP(3)R1 in the rat brain has been reported, the complete sequence of an IP(3)R1 clone from atrial myocytes has not been reported. We isolated an IP(3)R1 complementary DNA (cDNA) clone from isolated adult rat atrial myocytes, and found a new splice variant of IP(3)R1 that was different from a previously reported IP(3)R1 cDNA clone obtained from a rat brain (NCBI GenBank accession number: NM_001007235). Our clone had 99% similarity with the rat brain IP(3)R1 sequence; the exceptions were 39 amino acid deletions at the position of 1693-1731, and the deletion of phenylalanine at position 1372 that lay in the regulatory region. Compared with the rat brain IP(3)R1, in our clone proline was replaced with serine at residue 2439, and alanine was substituted for valine at residue 2445. These changes lie adjacent to or within the fifth transmembrane domain (2440-2462). Although such changes in the amino acid sequences were different from the rat brain IP3R1 clone, they were conserved in human or mouse IP3R1. We produced a plasmid construct expressing the atrial IP3R1 together with green fluorescent protein (GFP), and successfully overexpressed the atrial IP3R1 in the adult atrial cell line HL-1. Further investigation is needed on the physiological significance of the new splice variant in atrial cell function.