Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)

Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita

Research output: Contribution to journalArticle

23 Citations (Scopus)

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 languageEnglish
Pages (from-to)1758-1763
Number of pages6
JournalBioinformatics
Volume21
Issue number9
DOIs
Publication statusPublished - 2005 May 1

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Rice (Oryza sativa)
Site selection
Computational Analysis
Transcription
Gene expression
Exons
Genes
Tissue
Alternatives
Alternative Splicing
Transcription Initiation Site
Promoter
Gene Expression
Oryza
Gene
Polymerase Chain Reaction

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 journalArticle

Kitagawa, N, Washio, T, Kosugi, S, Yamashita, T, Higashi, K, Yanagawa, H, Higo, K, Satoh, K, Ohtomo, Y, Sunako, T, Murakami, K, Matsubara, K, Kawai, J, Carninci, P, Hayashizaki, Y, Kikuchi, S & Tomita, M 2005, 'Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)', Bioinformatics, vol. 21, no. 9, pp. 1758-1763. https://doi.org/10.1093/bioinformatics/bti253
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. / Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). In: Bioinformatics. 2005 ; Vol. 21, No. 9. pp. 1758-1763.
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