In mammalian spliceosome assembly, splicing factor 1 (SF1) and the 65 kDa subunit of U2AF (U2AF65) recognize branch point sequence(BPS) and polypyrimidine tract (PPT) respectively, which is important in forming the early E complex with U1 and the 35 kDa subunit of U2AF (U2AF35). 

In this paper, we propose a novel computational model (BPPT) integrating BPS and PPT characteristics for BPS prediction in human and other genomes. Specifically, a mixture model was used to infer the BPS motif and a novel scoring system was developed to estimate the affinity between U2AF65 and the query PPT sequence. BPPT was applied to all human introns to predict the candidate BPS. Analysis of the predicted BPS indicates that BPS with constitutive splice sites undergo more adaptive evolution. By estimating the relationships between predicted BPS, PPT, 5SS and 3SS in a set of orthologous introns, we find clue that BPS and PPT may co-evolve and coordinately facilitate the formation of spliceosome.