Splice sites are overrepresented in Pasilla binding motif clusters in D. melanogaster genes

For RNA-binding protein Pasilla, which has been shown to play a role in alternative splicing regulation, binding sites and clusters of binding sites are found in silico in the whole genome of D. melanogaster. The current study analyzes the occurrence of splice sites in binding site clusters. Several hundred thousand binding site motifs and thousands of significant motif clusters were identified. It was discovered that exonintron borders in D. melanogaster genes are reliably found within Pasilla binding motif clusters, with a higher frequency than could be otherwise expected based on a random model. Additionally, donor splice sites are found in Pasilla clusters twice as often as acceptor sites. This phenomenon is observed both for exons annotated as alternatively spliced and for exons annotated as constitutive. These observations support the hypothesis that Pasilla plays a functional role in splicing regulation of D. melanogaster.