Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).
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.
Kitagawa
Noriyuki
N
Institute for Advanced Biosciences, Keio University Tsuruoka, Yamagata, Japan.
Washio
Takanori
T
Kosugi
Shunichi
S
Yamashita
Tomoya
T
Higashi
Kenji
K
Yanagawa
Hiroshi
H
Higo
Kenichi
K
Satoh
Koji
K
Ohtomo
Yasuhiro
Y
Sunako
Tomomi
T
Murakami
Kazuo
K
Matsubara
Kenichi
K
Kawai
Jun
J
Carninci
Piero
P
Hayashizaki
Yoshihide
Y
Kikuchi
Shoshi
S
Tomita
Masaru
M
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*
D010940:Plant Proteins