The genomic sequence of the Atlantic salmon (Salmo salar) U2 snRNP-specific A' protein gene (U2A') was identified on a cosmid clone, and the exon/intron organization of a U2A' gene is described for the first time. The cosmid sequence includes 8 exons from which the 227 amino-terminal amino acids, of a total of 339 amino acids, are deduced. The cosmid cloning site was found in the 8th intron, which also contains a BglII minisatellite repeat region of unknown length. The 3' end of the gene was determined from a complementary DNA sequence. In the 234 amino-terminal amino acids the sequence identity is 84% to human and 49% to Arabidopsis thaliana. The phases of introns 1 to 8 are 1, 2, 0, 2, 0, 2, 0, and 1, respectively. The salmon U2A' gene was found by reverse transcription-polymerase chain reaction to be expressed in all 10 tissues tested, and in addition to the expected fragment of 695 bp, a smaller fragment of 615 bp was amplified in all tissues. Nucleotide sequencing of the fragments obtained showed that the smaller transcript lacks exon 6 and this results in frameshift of exon 7 and a truncated deduced polypeptide. This result may be explained by alternative splicing of the salmon U2A' gene. Different U2A' transcripts were found to exist also in human tissue.