Complementary DNA (cDNA) and gene for bovine retinal S-antigen have been isolated and characterized. cDNA clones were isolated from a Lambdagt11 cDNA expression library using polyclonal S-antigen antiserum and were further verified using monoclonal antisera. The largest cDNA observed was 500 base pairs long. This was used subsequently to screen cDNA clones from a Lambdagt10 retinal library, yielding fragments up to 900 base pairs in length. Polypeptides synthesized by the 500 base pair cDNA clone was recognized by 2 different monoclonal antibodies. In contrast, polypeptides produced by cDNA clones smaller than 400 base pairs were recognized by only one monoclonal antibody. The 500 base pair S-antigen cDNA was found to hybridize specifically to mRNA (approximately 1700 + 200 base pair) prepared from bovine retina and pineal gland but not to mRNA from liver, cerebral cortex and cerebellum. S-antigen was highly purified by HPLC and determined polypeptide sequence (19 AA) at near N-terminal. The DNA sequences of 500 and 900 base pair cDNA were determined using dideoxy method. 900 base pair cDNA covers the 240 amino acid residues from carboxyl terminal. The polypeptide deduced from DNA sequence is identical in sequence with known S-antigen peptides. The S-antigen polypeptide (240 AA residue) expressed in high yield expression bacterial system did not induce uveitis in the experimental animals. S-antigen and opsin probes were used for in situ hybridization analysis. S-antigen and opsin mRNAs were detected only rod cell inner segments and pinealocytes but not cone cells.