The unusually high levels of alternative splicing seen in the human brain, testis and liver prompted us to search for candidate tissue-specific splicing regulatory motifs in AS exons in genes expressed in each of these tissues. Using a procedure similar to Brudno et al. [59], sequence motifs four to six bases long that were significantly enriched in exons skipped in AS genes expressed in the human brain relative to constitutive exons in genes expressed in the brain were identified. These sequences were then compared to each other and grouped into seven clusters, each of which shared one or two four-base motifs (Table 2). The motifs in cluster BR1 (CUCC, CCUC) resemble the consensus binding site for the polypyrimidine tract-binding protein (PTB), which acts as a repressor of splicing in many contexts [60-63]. A similar motif (CNCUCCUC) has been identified in exons expressed specifically in the human brain [29]. The motifs in cluster BR7 (containing UAGG) are similar to the high-affinity binding site UAGGG [A/U], identified for the splicing repressor protein hnRNP A1 by SELEX experiments [64]. The consensus sequences for
