The predicted translation product of a cardiac AE3 mRNA contains an N terminus distinct from that of the brain AE3 Cl-/HCO3- exchanger. Cloning of a cardiac AE3 cDNA, organization of the AE3 gene, and identification of an alternative transcription initiation site.

We have isolated cDNAs encoding a cardiac variant of the AE3 Cl-/HCO3- exchanger from a rat heart library. The predicted cardiac AE3 polypeptide is 1030 amino acids in length, while the AE3 variant expressed in brain consists of 1227 amino acids. The C-terminal 957 amino acids of both polypeptides are identical, but the cardiac protein contains a unique N-terminal sequence of 73 amino acids which replaces the first 270 amino acids of the brain form. To determine the genetic basis for the differences between the cardiac and brain AE3 variants, we isolated and characterized the rat gene. Exons 1-6 contain the 5'-untranslated sequence and the first 270 codons of the brain mRNA, while exons 7-23 contain the coding and 3'-untranslated sequences which are common to the brain and cardiac mRNAs. The 5'-untranslated and unique N-terminal coding sequences of the cardiac mRNA are contained within a single exon, termed C1, which forms part of the intron between exons 6 and 7 of the brain transcription unit. Primer extension and S1 nuclease protection assays demonstrate that transcription of the cardiac AE3 mRNA precursor is intiaited within this intron. Therefore, alternative promoter and exon usage are involved in generation of the two AE3 mRNAs.