Identification and validation of splicing changes in EJC KD cells. (A) Venn diagrams showing the overlap between significant splicing events (cassette exons) identified with MISO and DiffSplice (left panels), using a threshold of 0.1 for ΔΨ. Correlation between the ΔΨ values predicted by MISO and DiffSplice are shown on the right, and Pearson’s correlation coefficient (r2) is indicated. (B,C) RT-PCR validation of two alternative exons (B) and one constitutive exon (C) in EJC and Upf1 KD cells. MRPL3 is predicted to increase in exon skipping (ΔΨ >0.1) in EJC KD whereas C20orf7 is predicted to increase in exon inclusion (ΔΨ <0.1) in EJC KD. KPNA1 is predicted to increase in exon skipping (ΔΨ >0.1) in EJC KD. The quantification of triplicate experiments are shown below as mean ± SD. ***P <0.001, one-way ANOVA.