Identical sequence patterns in the ends of exons and introns of human protein-coding genes

Intron splicing is one of the most important steps involved in the maturation process of a pre-mRNA. Although the sequence profiles around the splice sites have been studied extensively, the levels of sequence identity between the exonic sequences preceding the donor sites and the intronic sequences preceding the acceptor sites has not been examined as thoroughly. In this study we investigated identity patterns between the last 15 nucleotides of the exonic sequence preceding the 5′ splice site and the intronic sequence preceding the 3′ splice site in a set of human protein-coding genes that do not exhibit intron retention. We found that almost 60% of consecutive exons and introns in human protein-coding genes share at least two identical nucleotides at their 3′ ends and, on average, the sequence identity length is 2.47 nucleotides. Based on our findings we conclude that the 3′ ends of exons and introns tend to have longer identical sequences within a gene than when being taken from different genes. Our results hold even if the pairs are non-consecutive in the transcription order.

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► We examine the frequency of identical sequence patterns in the 3′ ends of exons and introns of human protein-coding genes.
► Genes having intron retention events detected in ESTs were purged from our analysis.
► The 3′ ends of exons and introns tend to have longer identical sequences within a gene than when being taken from different genes.