The complementary DNA (cDNA) for murine thromboxane synthase (TS) was isolated from a lung cDNA library. The full-length cDNA (1,910 bp) encodes a 533 amino acid protein (Mr 58,220) sharing 78% identity with human TS. Sequence comparison indicated that one of the two N-glycosylation sites, eight of the eleven cysteine residues, and a heme-binding domain are conserved in both murine and human TS sequences. The authenticity of the cDNA was confirmed by transient expression of a catalytically active TS in cos-1 cells. Northern analysis indicated that murine TS gene was expressed primarily in lung, kidney, and spleen. Interestingly, the size of mRNA in the kidney was approximately 100 to 150 bp shorter than that in the lung or spleen (2.2 Kb). RT-PCR and restriction mapping indicated that neither the coding sequence nor the 3' untranslated region could account for the observed size difference, suggesting a shorter 5' untranslated region and/or poly (A) tail in the kidney transcript.