Figure 1.

Distribution of pentamer pairs around constitutive exons. (a) Two intronic 50-nucleotide regions chosen on each side of an exon generate four possible pairings. Ud, upstream distal; Up, upstream proximal; Dp, downstream proximal; Dd, downstream distal. (b) The regions upstream and downstream of constitutive exons are highly correlated in GC content (Up and Dp shown here). The z-axis indicates the percent of exons whose combined 100-nucleotide flanks have the GC contents indicated on the x- and y-axes. (c) P-value distributions of constitutive exons and GC-balanced controls for the UpDp regions. The black line is the P-value distribution of constitutive exons with correction for GC content, the gray lines are the P-value distributions of ten GC balanced intron shuffled controls with correction for GC content, and the red dashed 45° line is the theoretical P-value distribution of the null hypothesis that the occurrences of upstream intronic motifs are independent of those of downstream intronic motifs. All P-value distributions of the ten controls matched the null hypothesis while the constitutive exons consistently generated substantially higher numbers of co-occurring motif pairs at different P-value cutoffs. The dashed black line is the P-value distribution for constitutive exons without correction for GC content. The dashed green line is the P-value distribution for the ten intron shuffled controls. These proportions without the correction are artifactually very high due to the high correlation of GC contents across limited genomic regions.