Features of the cassette exons regulated by PRPF40B. (A) Measurement of the 5′ss scores by maximum entropy model (MAXENT) for constitutive and alternative exons, regulated or not by PRPF40B, shows that PRPF40B-regulated exons have even weaker 5′ss than other alternative exons (Wilcoxon test). (B) MAXENT scores for 3′ss show that PRPF40B-regulated exons also have weaker 3′ss than background constitutive exons and other AS events (Wilcoxon test). (C) Lack of correlation between the strengths of the 5′ss of the PRPF40B-regulated cassette exons and their ΔPSI values in absolute numbers (t-test). (D) Cassette exons regulated by PRPF40B have shorter upstream but not downstream introns (Wilcoxon test). (E) The length of the PRPF40B-regulated cassette exons is similar to exons not regulated by PRPF40B (Wilcoxon test). (F) Top MEME motif found to be enriched in the PRPF40B-regulated cassette exons and flanking 200-nt-long intronic segments. The width of arrows indicates that the A-rich motifs are especially enriched in downstream introns. (G) Pol II inhibition assay in K562 WT, KO, and rescued cells. hnRNP DL exon 8 was used as a positive control because its inclusion increases upon slow transcription.
