A second cDNA for mouse brain 2',3'-cyclic-nucleotide 3'-phosphodiesterase (cDNAII) encoding 420 amino acids was isolated. The only difference from the cDNA obtained previously (cDNAI), which encodes 400 amino acids, was the 5'-end 53 bp. Comparison of the sequence of the mouse gene with the sequence of cDNAII indicates alternative splicing within exon 1. The 5'-end sequence of cDNAII was found in a region of the gene upstream of exon 1 and a second transcription initiation site was identified.