Two novel isoforms of the Ca2+/calmodulin-dependent protein kinase II delta subunit were detected in rat aorta. Identification of the subunits was based on two independent lines of evidence, i.e. detection by immunoblotting of differently sized delta subunits and DNA sequence analysis of partial cDNA clones of the kinase. Cytosolic extracts from rat brain, aorta, and cultured aortic cells were analyzed by Western blotting using a delta subunit-specific antipeptide antibody. Aortic extracts demonstrated a single 53-kDa cross-reactive band approximately 7 kDa smaller than the cross-reactive band seen in brain. To ascertain the structural basis for this difference, reverse-transcribed RNAs from rat aorta and brain were analyzed by polymerase chain reaction (PCR), and the PCR fragments were cloned and sequenced. When aortic cDNA was analyzed with a primer pair that spanned the known variable region of the brain kinase subunit, the amplified PCR products were smaller than the major product obtained from brain cDNA. The aortic PCR product was cloned and sequenced and found to represent two novel subunit sequences, designated delta 2 and delta 3 to distinguish them from the previously described delta sequence (now called delta 1) from brain. delta 2 was identical to the predicted delta 1 sequence except for a deletion of 102 base pairs (bp). This deletion corresponded to nearly the entire variable domain. In the sequence of delta 3, this 102-bp region was replaced by a sequence of 33 bp that had 79% nucleotide sequence identity to a portion of the gamma subunit variable domain. A fourth form of the delta subunit (delta 4) was identified in rat skeletal muscle. The delta 4 isoform was characterized by the deletion of a 42-bp sequence identical to the 42 bp at the 3' end of the 102-bp deletion of delta 2. Reverse-transcription PCR analysis of additional rat tissues indicated that alternatively spliced variants of the delta subunit of Ca2+/calmodulin-dependent protein kinase II are expressed in a tissue-specific pattern.