Fig. 2: Association between rs6410 genotype and intron 3 retention.
From: CYP11B1 variants influence skeletal maturation via alternative splicing
a Splice graph highlighting a local splicing variant (LSV) from exon 3. Blue junction represents skipping of exon 4; orange junction represents inclusion of exon 4; the green line represents retention of intron 3. Location of candidate SNP rs6410 is indicated and arrows indicate approximate locations for primers used for RT-PCR. Primer sequences are provided in Supplementary Data 8. b Scatterbox plot of MAJIQ quantifications for Percent Intron Retention (PIR) for intron 3 (green in the splice graph, cartoon in the plot inset), stratified by rs6410 genotype in GTEx. Boxes extend from the upper to lower quartile values of PIR per genotype and whiskers extend 1.5 times the interquartile range above the upper quartile and below the lower quartile. The line in the boxplot represents the group’s median value and the triangle represents the arithmatic mean. Legend indicates the Bonferonni adjusted P value for genotype effect and the expected change in PIR levels between homozygous C and homozygous T individuals. Source data for GTEx PIR values are available in Supplementary Data 9. c RT-PCR validation for the association between rs6410 genotype with intron 3 retention using six samples of adrenal hyperplasia from Erasmus MC (left) and nine samples from NIH (right). Primer locations and the expected products with sizes are shown on the left of the gels. Radiolabeled DNA ladder with known fragment sizes are included in the first lane of both gels. The full, uncropped gel images are available in Supplementary Fig. 8. Barplots below the gels indicate average PIR by genotype in each cohort with error bars indicating the sample standard deviation (where applicable) and show a significant association between rs6410 genotype and intron 3 retention in the Erasmus MC (Pearson r2 = 0.85, P = 0.009) and NIH (Pearson r2 = 0.91, P = 5.48 × 10−5) cohorts. Each samples’ PIR quantifcation is also included as a black dot on the barplot. Source data are available in Supplementary Data 10.
