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

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