Changes in splicing are observed between cells, tissues, organs and genomes. There is substantial variation in splicing associated with phenotypic differences in diverse organisms ranging from flowering time differences in plants to genetic diseases in humans. However, the underlying genetic architecture that regulates splicing variation is relatively less explored. We have exploited natural variation in diverse species to quantify splice-site usage for all splice-sites across the genome and uncovered variable splice sites. Exploiting projects such as the Genotype Tissue Expression (GTEx) project in humans, 1001 genome project (1001genomes) in Arabidopsis and the Drosophila Genotype Reference Panel (DGRP) project, we are mapping regulatory variation for splice-site usage by Genome Wide Association Studies (GWAS) across tens of thousands of splice-sites. This work directly links genetic variation with the usage of specific individual splice-sites. The individual splice-site usage analysis increases the resolution at a highest level, which allows mining causal variants for genome-wide patterns that govern splice-site choice. By analysing common patterns, we are able to decipher an evolutionarily conserved features that form the basic vocabulary of the splicing code.