Abstract
Motivation: Transcription start site selection and alternative splicing greatly contribute to diversifying gene expression. Recent studies have revealed the existence of alternative first exons, but most have involved mammalian genes, and as yet the regulation of usage of alternative first exons has not been clarified, especially in plants. Results: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using RT-PCR, and searched for the promoter elements that might regulate the alternative first exons. As a result, we detected a number of unreported alternative first exons, some of which are regulated in a tissue-specific manner.
| Original language | English |
|---|---|
| Pages (from-to) | 1758-1763 |
| Number of pages | 6 |
| Journal | Bioinformatics |
| Volume | 21 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - 2005 May 1 |
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ASJC Scopus subject areas
- Clinical Biochemistry
- Computer Science Applications
- Computational Theory and Mathematics
Cite this
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). / Kitagawa, Noriyuki; Washio, Takanori; Kosugi, Shunichi; Yamashita, Tomoya; Higashi, Kenji; Yanagawa, Hiroshi; Higo, Kenichi; Satoh, Koji; Ohtomo, Yasuhiro; Sunako, Tomomi; Murakami, Kazuo; Matsubara, Kenichi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Kikuchi, Shoshi; Tomita, Masaru.
In: Bioinformatics, Vol. 21, No. 9, 01.05.2005, p. 1758-1763.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)
AU - Kitagawa, Noriyuki
AU - Washio, Takanori
AU - Kosugi, Shunichi
AU - Yamashita, Tomoya
AU - Higashi, Kenji
AU - Yanagawa, Hiroshi
AU - Higo, Kenichi
AU - Satoh, Koji
AU - Ohtomo, Yasuhiro
AU - Sunako, Tomomi
AU - Murakami, Kazuo
AU - Matsubara, Kenichi
AU - Kawai, Jun
AU - Carninci, Piero
AU - Hayashizaki, Yoshihide
AU - Kikuchi, Shoshi
AU - Tomita, Masaru
PY - 2005/5/1
Y1 - 2005/5/1
N2 - Motivation: Transcription start site selection and alternative splicing greatly contribute to diversifying gene expression. Recent studies have revealed the existence of alternative first exons, but most have involved mammalian genes, and as yet the regulation of usage of alternative first exons has not been clarified, especially in plants. Results: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using RT-PCR, and searched for the promoter elements that might regulate the alternative first exons. As a result, we detected a number of unreported alternative first exons, some of which are regulated in a tissue-specific manner.
AB - Motivation: Transcription start site selection and alternative splicing greatly contribute to diversifying gene expression. Recent studies have revealed the existence of alternative first exons, but most have involved mammalian genes, and as yet the regulation of usage of alternative first exons has not been clarified, especially in plants. Results: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using RT-PCR, and searched for the promoter elements that might regulate the alternative first exons. As a result, we detected a number of unreported alternative first exons, some of which are regulated in a tissue-specific manner.
UR - http://www.scopus.com/inward/record.url?scp=20844441941&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=20844441941&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/bti253
DO - 10.1093/bioinformatics/bti253
M3 - Article
C2 - 15647298
AN - SCOPUS:20844441941
VL - 21
SP - 1758
EP - 1763
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 9
ER -