Fig. 1: RNA-seq analysis of Rbm4dKO embryonic brain.

A Pie chart shows alternative splicing events identified in the E13.5 Rbm4dKO brain. The percentage and event number of each category are indicated. B Schematic depicts cassette exon selection (CES). Volcano plot of CES: the x-axis represents the difference of percent spliced in (∆PSI: PSI^Rbm4dKO-PSI^WT); the y-axis indicates the negative log10 transformation of false discovery rate (FDR). Red dots represent differentially expressed CES events with statistical significance (FDR < 0.005). Transcripts indicated were subjected to RT-PCR analysis (see Fig. 2) (black, exon skipping; blue, exon inclusion). Orange indicates the transcripts with a ∆PSI value of 1.0 or −1.0. C Gene Ontology analysis of the CES category. The x-axis represents the negative log10 transformation of the P-value; the y-axis indicates the top-ranked terms in the CES category. D Schematic depicts intron retention (IR). Volcano plot of the IR category: the x-axis indicates the difference in percent intron retention (∆PIR: PIR^Rbm4dKO-PIR^WT); the y-axis is the same as in (B). Red dots represent differentially expressed IR events with FDR < 0.005. Orange indicates the transcripts with a ∆PIR value of 1.0. E Gene Ontology analysis of the IR category; the x-axis is the same as in (C); the y-axis indicates the top-ranked terms in the IR category. F Intron length distribution comparison between genome introns (n = 490290) and RBM4-regulated introns (n = 399). G The GC content of genome introns and RBM4-regulated introns. Bars represent average ± SEM (***P < 0.001).