Natural rules for Arabidopsis thaliana pre-mRNA splicing site selection

The accurate prediction of plant pre-mRNA splicing sites has been studied extensively. The rules for plant pre-mRNA splicing still remain unknown. This study, based on confirmed sequence data, systematically analyzed all expressed genes on Arabidopsis thaliana chromosome IV to quantitatively explore the natural splicing rules. The results indicated that defining Arabidopsis thaliana pre-mRNA splicing sites required a combination of multiple factors including (1) relative conserved consensus sequence at splicing site; (2) individual nucleotide distribution pattern in 50 nucleotides up- and down-stream regions of splicing site; (3) quantitative analysis of individual nucleotide distribution by using the formulations concluded from this study. The combination of all these factors together can bring the accuracy of Arabidopsis thaliana splicing site recognition over 99%. The results provide additional information to the future of plant pre-mRNA splicing research.