Constraints acting on the exon positions of the splice site sequences and local amino acid composition of the protein

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Abstract
The exon positions located at the 5′ and 3′ splice sites are involved in two functions: in the accurate removal of introns from the nuclear pre-messenger RNAs and in coding for amino acids. Therefore, at least two constraints will act on the exon positions: the splicing constraint and the protein constraint. In the present study we investigate the effect of those constraints on a set of splice sites extracted from GenBank. The consensus matrices computed for each intron location in the reading frame present striking differences at the exon positions of the 5′ splice sites. The results obtained can not be explained by the action of a single constraint but rather by the competition between the splicing and protein constraints. Out of eight sites corresponding to codons located in the vicinity of the intron, three present an amino acid distribution that differs greatly from the average amino acid composition of the proteins. Each of these three sites can be characterized by specific amino acids. Results show that the splicing constraint has an effect on the local amino acid composition of the protein as long as the function of the protein is not disrupted.

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