The amino acid sequence of the rat 40S ribosomal subunit protein S3a was deduced from the sequence of nucleotides in two recombinant cDNAs and confirmed by the determination of the NH2-terminal sequence by Edman degradation. Ribosomal protein S3a has 263 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and the molecular weight is 29,794. The protein designated S3b has the same amino acid sequence as S3a except that it lacks the carboxyl-terminal 12 residues. We are unable to determine whether there are separate genes for S3a and S3b, or whether there is a single gene and alternate splicing of the precursor to yield separate mRNAs for S3a and S3b, or whether there is a single gene and a single mRNA whose translation yields S3a which is converted by proteolysis, either physiological or fortuitous, to S3b. The mRNA for S3a is about 1000 nucleotides in length. Hybridization of cDNA to digests of nuclear DNA suggests that there are 8-13 copies of the S3a gene. Rat ribosomal protein S3a is identical to the product of the rat Fte-1 gene which encodes the V-Fos transformation effector; S3a is also related to the plant protein cyc07, which is encoded by a cell cycle S-phase specific gene.