Alternative splices capable of generating proteins with altered functions were found (by PCR) in isoform 2 of the rat plasma membrane Ca2+ pump. These splices were concentrated in two hypervariable regions. One of these regions, near the N-terminus and the lipid-binding region, could be altered by the insertion of either or both of inserts x and y. Insertion of both x and y would add 45 amino acids to the molecule. The y insert causes the appearance of a rather hydrophobic stretch of amino acids in the middle of a highly polar region. The second variable region begins in the middle of the calmodulin-binding domain. Insertion of 229 nucleotides at this point of the message converts the b form to the a form, which has an altered (and shorter) C-terminus. The calmodulin-binding domain of this shortened form has a less basic character, which would decrease the affinity for calmodulin. The b form of isoenzyme 2 contains relatively weak protein kinase A substrate sequences, such as KQNSS and KNNS. These sequences are eliminated in form a, and a strongly activated kinase substrate sequence, RRQSS, appears in a different place. Different tissues use different combinations of alternative splices, with heart and brain showing the greatest diversity.