FIG. 2.

Cryptic 5' splice sites are underrepresented in introns. (A) The distribution of asymmetry values for all possible 4096 hexamers across the introns of Drosophila melanogaster. The distribution of asymmetry scores is symmetrical around 0 because each motif and its reverse complement have the same value but with opposite signs. The asymmetry against the motif G|GTAAG (−0.288) is six standard deviations off the mean of the distribution. Arrows indicate the top three values belong to 6mers that overlap the 9 bp of the consensus 5′ splice site, CAG|GTAAGT. Importantly, the next most significant value over laps the motif CAG|GTGAGT, indicating selection against both AA and GA cryptic splice sites (supplementary fig. 1, Supplementary Material online). (B) Motifs present at high frequency at actual 5′ splice sites show high asymmetry within D. melanogaster introns. This indicates that selection targets a large number of motifs that may compete during splicing, and it follows that introns with generally weak splice sites will be sensitive to competition from a larger number of potential cryptic splice sites. Number of motifs shown is all possible 4096 hexamers.