NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning

Small first introns show a bias for increased intron retention after Salsa depletion. (A) Proportion of first (white) and all other (gray) introns within each intron class, with the number of first introns/number of other introns indicated on top/bottom of each bar in color/black, respectively. (B–G) Violin plots and boxplots (highlighting the median, 25th and 75th percentiles per intron class) summarizing distributions of observations (each point refers to one intron) considering all introns (left panels) and first introns only (right panels) of: (B,C) log₁₀ of intron length (nt); (D,E) log₁₀ of distance (nt) between intron start and the transcript transcription start site (TSS); (F,G) Maximum entropy (MaxEnt) scores (Yeo and Burge 2004) for estimation of 3′ splice site efficiency, obtained with MATT (Gohr and Irimia 2019). Comparison of metrics in B–G was performed with Affected as the reference: (*) P < 0.05, (**) P < 0.01 and ns, nonsignificant (Wilcoxon rank-sum test with continuity correction).