Fig. 5.

Analyses of the tendencies of Pol II pausing predicted by PEPMAN on different alternative splicing (AS) events, including (A) skipping exons (SEs), (B) mutual exclusive exons (MXEs), (C) retained introns (RIs), (D) alternative $3\prime$ splice sites (A3SSes), and (E) alternative $5\prime$ splice sites (A5SSes). In each panel, the lower indicates the splicing types, while the upper shows the PEPMAN prediction scores on the corresponding splice sites. Each color represents a single exon, and each box plot represents the normalized prediction scores on the corresponding exon–intron boundary. Introns are represented by lines, and the RI in C is represented by a light blue box. The PEPMAN prediction scores of 3′SSes and 5′SSes in individual AS events are normalized by the median of the prediction results of the corresponding splice sites from 5,000 randomly selected constitutive exons. *: $1\times 10^{-10}<P<0.001$, two-sided Wilcoxon rank-sum test; **: $P<1\times 10^{-10}$, two-sided Wilcoxon rank-sum test; ^-: $P>0.001$, two-sided Wilcoxon rank-sum test.