Fig. 6

Introns that are retained and exons that are differentially used after PRPF8 depletion have weak 5′ splice sites. a Inefficiently spliced introns have weaker 5′ splice sites. A set of 200 retained introns (RI) were selected based on fold-change differences (see “Materials and methods”), and non-retained introns (NRI) within the same set of genes were used as a contrast. A 5′ splice site strength analysis was then carried out as described in “Materials and methods” for each subset. Statistically significant pairwise comparison is indicated (**p < 0.01). b Motif enrichment analysis on the same set of genes shows that although the most frequently identified motifs correspond to the consensus splice site sequences for both retained (RI) and non-retained introns (NRI), the percentage of targets with such motifs varies significantly between the two categories (68.50 % for RI versus 91.03 % for NRI; p < 2.2 × 10⁻¹⁶, Fisher’s exact test). c Analysis of GC composition reveals that retained introns have higher GC content than non-retained introns with values closer to those of adjacent exons. Differential GC content was calculated by dividing GC content of each intron to the average of its adjacent exons (see “Materials and methods”). Statistically significant pairwise comparison is indicated (***p < 0.001). d Differentially used exons have weaker 5′ splice sites. A 5′ splice site strength analysis was carried out as described in “Materials and methods” for each subset. Statistically significant pairwise comparison is indicated (***p < 0.001)