Previous work indicated that there was a large difference of the sequence features of introns between highly- and lowly-transcribed yeast genes. Some potential positive transcriptional regulatory motifs in the highly-transcribed introns were extracted. It was found that these introns were very close to the upstream regions of genes, and several introns even located within 5'-UTR. These results show that introns of yeast genes may regulate the transcriptional efficiencies and cooperate with upstream regions. To understand the synergy between upstream regions and introns of highly-transcribed yeast genes, the upstream regions (800 bp upstream of translation start sites, or the regions of two adjacent genes) of these two sets of genes were retrieved, and some potential positive transcriptional motifs in the upstream of highly-transcribed genes were extracted using the statistical comparative analysis approach developed before. Most of the potential motifs extracted were supported by literature search of experimental analyses. Then, every pair of oligonucleotides, one in the upstream region and the other in the intron, was defined as an "oligonucleotide pair", i.e. a motif pair. Considering the motif pairs with the "nearest distance" not larger than 84 bp, the motif pairs, mainly tetra- and penta-nucleotide pairs, occurring in the highly-transcribed genes non-randomly were extracted and the synergistic pattern of these motif pairs including position distributions and binding transcription factors such as RAP1, ABF1 and TAF was analyzed. Some potential patterns of transcriptional synergy were observed. These results could help people to understand the mechanism of transcriptional regulation and provide evidence for biological verification.