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

• Published in: Bioinformatics Vol. 21; no. 9; pp. 1758 - 1763
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.05.2005; Oxford Publishing Limited (England)
• Subjects: Alternative Splicing - genetics; Biological and medical sciences; Chromosome Mapping - methods; Computer Simulation; Evolution, Molecular; Exons - genetics; Fundamental and applied biological sciences. Psychology; General aspects; Genetic Variation - genetics; Genome, Plant; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Genetic; Oryza - genetics; Oryza - metabolism; Oryza sativa; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Structures - genetics; Plant Structures - metabolism; Tissue Distribution; Transcription Initiation Site; Transcriptional Activation - genetics; Site; Alternative splicing; Monocotyledones; Transcription; Selection; Gene expression; Oryza sativa; Tissue; Vertebrata; Exon; Mammalia; Gramineae; Angiospermae; Spermatophyta; Rice
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti253

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