Computational analysis of candidate exonic splicing regulatory motifs in rice
| Autor: | Yan-Kai Wang, 王彥凱 |
|---|---|
| Rok vydání: | 2009 |
| Druh dokumentu: | 學位論文 ; thesis |
| Popis: | 97 Exonic splicing enhancers (ESEs), known as a kind of specific short oligonucleotides, appear in the exon and enhance pre-mRNA splicing. Although plant SR proteins and their functions have been studied, there is limited information about plant ESE elements. In this research, we used statistical methods to predict candidate rice ESE elements. We compared the frequency of occurrence of hexamers (6-mers) in two cases, i.e., exons versus introns, and exons with weak splice site versus exons with strong splice site. 115 candidate ESE motifs were identified and many of them match previously reported ESE sequences. Rice-specific putative ESE motifs were also identified in the study. Finally, we characterized the distribution of ESE in rice pre-mRNAs. It was found that candidate ESEs present at a higher density within intron retentions compared with introns. Density of some of candidate ESEs in exons was higher than UTR. Additionally the exons show higher ESE density in the vicinity of acceptor splice site and in the middle of exon. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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