The upstream activating sequence (UAS) of TDH3, one of three genes encoding glyceraldehyde phosphate dehydrogenase in Saccharomyces cerevisiae, was characterized by using a series of external and internal deletion mutants of the TDH3 upstream region. The levels of activation by these deletions of transcription mediated through either the segment of TDH3 promoter or the segment of ADH1 (alcohol dehydrogenase 1 gene) promoter were quantitatively examined and the region between -583 and -447 was found to be required for full transcriptional activation with either promoter segment. It has been demonstrated that the protein binding site involved in the formation of two DNA-protein complexes is identical with the consensus RAP1 binding sequence by methylation interference assay. Surprisingly, the UAS fragment composed of the 22-mer sequence containing exclusively a RAP1 binding sequence showed full activation, suggesting that the RAP1-dependent transcriptional activation is a primary positive control in the TDH3 gene expression. In addition, a pair of inverted repeat sequences homologous to the binding sequence for GRF2, another yeast trans-acting factor, and directly repeated sequences containing a CATCC motif were also found upstream and downstream, respectively, of the RAP1 binding site. Deletion analysis suggested that these elements could also function as regulatory elements for transcription.