Splice isoform classes are differentially affected by loss of UPF2. (a) Schematic drawing of the main isoform classes detected in our pipeline. (b) RT-PCR validation of 25 splicing events predicted from our pipeline (see Table S9 in Additional file 12 for a list of the 49 validated events out of 50 tested). Top: normal AS events. Middle: PTC upon inclusion events. Bottom: PTC upon exclusion by ES. (c) Western blotting from two different liver pairs, showing UPF2 (rabbit α-UPF2), SRp55, SRp40 and SRp30 (mouse α-mAb104) and β-actin (rabbit α-actin). The asterisk denotes the truncated UPF2 isoform found in cells ablated for NMD. (d) MXE splicing of Pkm2 and the inclusion of both mutually exclusive exons in the KO sample.