Experimental support of predicted functional SNPs. (A) Minigene experiments validating predicted functional SNPs for GMAS in triplicates (R1–3). The inclusion levels (% inclusion) of the skipped exons or retained introns were estimated from the band intensities of the PAGE gel. Note that, for illustration purposes, the y-axis scales are different for different genes. (B) eCDF of the absolute changes in the PSI values of GMAS exons upon KD of splicing factors associated with putative functional SNPs (based on motif analysis or eCLIP overlap). All splicing factors in Supplemental Figure S9A with ENCODE KD RNA-seq data are included here. The P-value was calculated using the Kolmogorov–Smirnov test. (C) EMSA validating allele-specific binding of BUD13 to putative functional SNPs. The amount of BUD13 protein used in the experiment is illustrated above the gel. BUD13 eCLIP reads (gray) are shown below the gel, where the locations of the SNPs are labeled with vertical colored lines. The fraction of reads supporting either allele at the functional SNP position is delineated.