title: Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  http://www.bioinfo.sfc.keio.ac.jp/research/intron.
authors.affiliation: Institute for Advanced Biosciences, Keio University Tsuruoka, Yamagata, Japan.
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Kitagawa
authors.forename: Takanori
authors.initials: T
authors.lastname: Washio
authors.forename: Shunichi
authors.initials: S
authors.lastname: Kosugi
authors.forename: Tomoya
authors.initials: T
authors.lastname: Yamashita
authors.forename: Kenji
authors.initials: K
authors.lastname: Higashi
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yanagawa
authors.forename: Kenichi
authors.initials: K
authors.lastname: Higo
authors.forename: Koji
authors.initials: K
authors.lastname: Satoh
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Ohtomo
authors.forename: Tomomi
authors.initials: T
authors.lastname: Sunako
authors.forename: Kazuo
authors.initials: K
authors.lastname: Murakami
authors.forename: Kenichi
authors.initials: K
authors.lastname: Matsubara
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Shoshi
authors.initials: S
authors.lastname: Kikuchi
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D018745:Genome, Plant; D008957:Models, Genetic; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018514:Plant Structures / Q000235:genetics* / Q000378:metabolism; D014018:Tissue Distribution; D024363:Transcription Initiation Site; D015533:Transcriptional Activation / Q000235:genetics*
chemical_list: D010940:Plant Proteins