Quantifying splice-site usage: a simple yet powerful approach to analyze splicing

Abstract RNA splicing, and variations in this process referred to as alternative are critical aspects of gene regulation eukaryotes. From environmental responses plants being a primary link between genetic variation disease humans, splicing differences confer extensive phenotypic changes across diverse organisms (1–3). Regulation occurs through differential selection splice sites reaction, which results the abundance isoforms and/or events. However, genomic determinants that influence splice-site remain largely unknown. While traditional approaches for analyzing rely on quantifying variant transcripts (i.e. isoforms) or events intron retention, exon skipping etc.) (4), recent focus complex/mutually exclusive patterns (5–8). none these explicitly measure individual usage, can provide valuable information about choice its regulation. Here, we present simple approach quantify empirical usage reflecting their strength, determines reaction. Splice-site strength/usage, quantitative phenotype, allows us directly with splice-sites. We demonstrate power defining GWAS. Our pilot analysis more than thousand hints sequence divergence cis rather trans is associated among accessions Arabidopsis thaliana. This deciphering principles has broad implications from agriculture medicine.