Abstract: Transcriptional regulation in eukaryotic genes generally requires combinatorial binding on DNA of multiple transcription factors. Though many analyses have been performed for identification of combinatorial patterns in promoter sequences, there are few studies concerned with introns of genes. Here our study focuses on the transcriptional synergistic (cooperative) regulation between upstream promoters and introns of ribosomal protein (RP) genes in Saccharomyces cerevisiae yeast. We first extract some potential transcriptional regulatory motifs based on a statistical comparative analysis. 98% of these motifs are accordance with experimental analyses. Then by pairing these motifs each other, we identify some potential synergistic motif pairs between upstream regions and introns of yeast RP genes (RPGs). Among 48 detected motif pairs, 44 match the binding sites for interacting transcriptional factors known from experiments or predictions. Checking the positions of these motif pairs in yeast RPGs, it is found that both motifs of the detected motif pairs are enriched in specific regions of upstream regions and introns, respectively. Some motif pairs present distance and orientation preferences, which may be favorable for transcription factors to bind simultaneously to DNA. These results will be helpful to understand the mechanism of synergistic regulation in yeast RPGs.CI - Copyright (c) 2010 Elsevier Ltd. All rights reserved.