New analytical tool for analysis of splice site sequence determinants

A new analytical method has been used to examine the set of 40 exon/intron boundaries within the rat embryonic myosin heavy chain (MHCemb) gene and work out a more detailed set of recognition sequence requirements for the splicing of nuclear pre-mRNA.

Abstract

A new analytical method has been used to examine the set of 40 exon/intron boundaries within the rat embryonic myosin heavy chain (MHCemb) gene. It has also been applied to an additional set of 850 splice sequences selected from GenBank. Strong evidence is obtained for the involvement of 3' ends but not 5' ends of exon sequences in splice site recognition. It can be determined that signal sequences of 5' intron ends concentrate near the splice borders, while the distributions of the 3' intron ends have a diffuse character. The possibility of re-interpreting some known features, in terms of the absence of certain elements rather than the presence of elements forming sequence determinants, is discussed. The analysis undertaken enabled us to work out a more detailed set of recognition sequence requirements for the splicing of nuclear pre-mRNA. In addition to requirements which have already been established we suggest the following: the 'AG-absence' in the immediate 3' terminal intron sequences; and a minimal match between a particular sequence and the known exon/intron consensus sequence of 5' splice junctions.