Elongation factor-1 alpha (EF-1 alpha) is a highly conserved protein functioning in peptide elongation during translation. A cDNA, S1, was isolated; its deduced amino acid sequence shares high similarity with mammalian EF-1 alpha s (92%). While EF-1 alpha is present in all tissues, S1 mRNA can only be detected in brain, heart, and muscle. We report here that the retropseudogene phenomenon is attributable to EF-1 alpha and not S1, the latter being represented by a single copy in the rat genome. The S1 steady-state mRNA levels are consistently higher than EF-1 alpha in S1-positive tissues. S1 mRNA can only be detected late during brain, heart, and muscle development in vivo and increases to a plateau in early postnatal life. In a cultured muscle system, S1 expression is dependent upon the formation of myotubes, although the accumulation of S1 mRNA is significantly lower than that observed in adult skeletal muscle. EF-1 alpha mRNA levels are down-regulated during brain, heart, and muscle development, but stay relatively steady in liver. We show here that EF-1 alpha and S1 are differentially expressed during rat development and that the activation of S1 gene expression is subsequent to the terminal differentiation process in brain, heart, and muscle.