A single gene appears to code for the inositol 1,4,5-trisphosphate receptor (itpr) in Drosophila melanogaster, as compared to three known genes in mammals. Expression of the itpr gene in Drosophila occurs in a wide range of tissues and developmental stages, suggesting its requirement during diverse cellular and physiological processes. A head cDNA for the Drosophila IP3R has previously been cloned and sequenced. Here we present and analyse the sequence of cDNAs encoding the complete IP3R, obtained from embryonic stages. The embryonic cDNA is 10525bp long and is a splice variant of the head cDNA. It differs from the latter in three main respects. It has longer 5' and 3' untranslated regions, two potential casein kinase II sites are missing in the embryo form and it contains an alternate exon which results in the replacement of three residues (VHF) in the head form by five residues (GVGHSV) in the embryo form. The significance of these changes is discussed. An exon-intron map of the gene derived from sequencing of intron-containing genomic fragments is also presented. The gene has a total of 11 introns, of which more than half are clustered in a region of the modulatory domain of the IP3R.