Characteristics of EJC-dependent exons. (A) Box plot of intron lengths for flanking introns, comparing EJC-dependent exon inclusion (+), exon skipping (−) and exons without splicing changes (Ctr). The P value is calculated with Mann–Whitney-Wilcoxon Test, and is indicated. (B) Box plot of intron lengths for flanking introns, comparing EJC-dependent constitutive exons (Con) and EJC-independent constitutive exons (Ctr Con). (C) RNA splicing map showing the normalised eIF4A3 CLIP reads in the upstream exon, cassette exon and downstream exon, 100 nt from the exon-intron border. EJC-dependent exon inclusion (+) are shown as red, exon skipping (−) are shown as blue, and control exons with has no splicing changes are shown as grey. The CLIP reads were normalised to mRNA expression level and exon length, and the height of CLIP reads at a position is the sum of all normalised CLIP reads at that position for each category of exons.