We report here the isolation and characterization of cDNA clones for a novel isoform of CDCrel-1 septin, termed CDCrel-1A, with a different 5' end sequence from the transcripts encoding the known CDCrel-1 (designated as CDCrel-1F) in the developing rat neocortex, Alternative polyadenylation site selections resulted in various transcripts for CDCrel-1A including the fusion forms with another gene, platelet glycoprotein Ib beta (GPIb beta). Expression of the distinct transcripts encoding CDCrel-1A and CDCrel-1F increased and decreased, respectively, from the infant to adult period, Therefore CDCrel-1A might be a major form of the CDCrel-1 septin in the adult neocortex of mammals.