Fig. 6

a Bar plot of the proportion of unannotated (cryptic) last exons from mouse cortical neurons grouped based on their regulation by Sfpq. Two-sided Fisher’s exact test was performed. b Introns from mouse CLE-expressing genes were scored by their relative length and the distribution of these scores were plotted. The box bounds represent the first and third quartiles and the black lines at the middle of the boxes show the medians. Top and/or bottom whiskers represent 1.5x of the range between the third and the first quartiles (interquartile range). Circles represent outliers. Two-sided Wilcoxon rank-sum test was performed. c Metaplot of the mean number of Sfpq CLIP peaks (±SEM) in region surrounding cryptic last exons or constitutive last exons of the same gene (control). d, e CLIP-seq peak distribution (top) and RNA-seq coverage plots (mid) from representative CLE-containing introns. The Y-axis scale of the read coverage plots is optimized for CLE/intronic reads. Sequence homology of flanking exons from orthologous CLE-containing genes is compared and the relative position of zebrafish CLEs is shown at the bottom. f Heatmap illustrating increased inclusion (ΔPSI) of 68 CLEs upregulated in ALS-mutant background at different stages of neuronal differentiation. ΔPSI values of non-significant events are set to 0. Induced pluripotent stem cells (iPSC); neural precursors (NPC); “patterned” precursor motor neurons (ventral spinal cord; pMN); post-mitotic but electrophysiologically immature motor neurons (MN); electrophysiologically mature MNs (mMN). g Representative RNA-seq coverage plots from ALS-derived iPSC dataset of CLEs upregulated in VCP^mu samples.