Fig. 2. Example of the utility of splicing quantitative trait loci for interpretation of trait-associated loci. (A) Boxplot of expression ratio of the exon with alternative 3-prime splicing site between phenotypes of the polymorphism, located in chr3:20536243. The expression ratio is higher in the heterozygote. (B) This is the predicted protein structure of the AT3G55400 gene using the RaptorX web-based tool [16]. The alternative 3-prime splicing site leads to the loss of alpha helices (yellow arrow). (C) The single nucleotide polymorphism, a 3′-untranslated region variant, likely leads to an alternative 3′ splicing site.