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Bioinformatics Advance Access originally published online on January 12, 2005
Bioinformatics 2005 21(9):1758-1763; doi:10.1093/bioinformatics/bti253
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

Noriyuki Kitagawa 1,3, Takanori Washio 1,4,*, Shunichi Kosugi 1, Tomoya Yamashita 1,3, Kenji Higashi 1,3, Hiroshi Yanagawa 1, Kenichi Higo 5, Koji Satoh 5, Yasuhiro Ohtomo 6, Tomomi Sunako 6, Kazuo Murakami 6, Kenichi Matsubara 6, Jun Kawai 7, Piero Carninci 7, Yoshihide Hayashizaki 7, Shoshi Kikuchi 5 and Masaru Tomita 1,2

1Institute for Advanced Biosciences, Keio University Tsuruoka, Yamagata 997-0035, Japan
2Department of Environmental Information, Keio University Fujisawa, Kanagawa 252-8520, Japan
3Graduate School of Media and Governance, Keio University Fujisawa, Kanagawa 252-8520, Japan
4Graduate School of Information Science, Nara Institute of Science and Technology Ikoma, Nara 630-0192, Japan
5National Institute of Agrobiological Sciences Tsukuba, Ibaraki 305-0062, Japan
6Foundation for Advancement of International Science (FAIS) Tsukuba, Ibaraki 305-0062, Japan
7Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC) Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

*To whom correspondence should be addressed.

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.

Contact: washy{at}sfc.keio.ac.jp

Supplementary information: http://www.bioinfo.sfc.keio.ac.jp/research/intron


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