A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.

ABSTRACT:

Background

Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites.

Results

We have developed a new computational technique to identify significantly conserved motifs involved in splice site regulation. First, 84 putative exonic splicing enhancer hexamers are identified in Arabidopsis thaliana. Then a Gibbs sampling program called ELPH was used to locate conserved motifs represented by these hexamers in exonic regions near splice sites in confirmed genes. Oligomers containing 35 of these motifs have been shown experimentally to induce significant inclusion of A. thalian

SUBMITTER: Pertea M 

PROVIDER: S-EPMC1892810 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature