alpha-Tocopherol transfer protein (alpha TTP) present in rat liver cytosol specifically binds this vitamin and enhances its transfer between separate membranes. We previously reported purification of alpha TTP and showed that two isoforms exist in rat liver, of which the isoelectric points are 5.0 and 5.1, respectively (Sato, Y., Hagiwara, K., Arai, H., and Inoue, K. (1991) FEBS Lett. 288, 41-45). In the present paper, we have isolated a cDNA clone with 2194 base pairs encoding alpha TTP from a rat liver cDNA library. The amino acid sequence deduced from the cDNA contained all the sequences of the peptide fragments obtained by digestion of the purified protein with endoproteinase Lys-C. The isolated cDNA was found to encode the isoform with a pI of 5.0 on the basis of the cross-reactivity of the recombinant protein expressed in Escherichia coli with the isoform-specific monoclonal antibody. From the longest open reading frame of the cloned cDNA, one isoform of rat liver alpha TTP is predicted to be composed of 278 amino acid residues of calculated molecular weight 31,845. Both Western and Northern blot analyses revealed that alpha TTP is expressed exclusively in the liver in rats. alpha TTP has been found to exhibit a structural homology with the cellular retinaldehyde-binding protein present only in visual tissues.