Mutually exclusive and cassette exons underlie alternatively spliced isoforms of the Na/Ca exchanger

We have analyzed the gene structure that gives rise to tissue-specific isoforms of the Na/Ca exchanger. Five distinct isoforms of the Na/Ca exchanger from rabbit brain, kidney, and heart have been identified previously to which we now add a new brain isoform. Reverse-transcribed polymerase chain reaction, library screening, and sequence analysis of cDNA coding regions indicate that the only significant alteration of the Na/Ca exchanger cDNA in rabbit brain, kidney, and heart isoforms is located in the carboxyl end of the putative intracellular loop of the protein, a region recently linked to ionic and metabolic regulation of the Na/Ca exchanger. Additionally, we find that the Na/Ca exchanger isoforms found in lung and skeletal muscle may arise from among these same six isoforms. Examination of the gene structure of the Na/Ca exchanger in rabbit indicates how the single gene that encodes for the Na/Ca exchanger is alternatively spliced to give rise to the five rabbit isoforms. Specifically, sequence analysis of the intron-exon boundaries reveals the presence of two 'mutually exclusive' exons in conjunction with four 'cassette' exons in the region of the Na/Ca exchanger gene that codes for the carboxyl end of the predicted intracellular loop region. This unusual arrangement of exons in the Na/Ca exchanger gene could allow for the generation of up to 32 different Na/Ca exchanger mRNAs and accounts for the isoforms identified to date.