Possible role of nucleotide correlations between human exon junctions

Abstract There is ample evidence that prediction of human splice sites can be refined by analyzing the nucleotides surrounding splice sites. This could mean that exon nucleotides over splice sites harbour information for the splicing process in addition to the coding information to specify aminoacids. We analyzed the correlations among the nucleotides lying at the end and at the beginning of all the consecutive human exons to seek relationships among the nucleotides. We have divided the sequences taking into account the phase of interruption. Even though exon sequences are involved in the coding function, we found phase-dependent, specific correlations in the area of exon junctions. These regularities do not give rise to specific motifs, but rather to a phase-specific nucleotide context that could contribute to define the splice site or aid the splicing machinery to join the exon ends. Results provide further evidence that accurate selection of human splice sites likely requires the contribution of exon regulatory sequences.