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Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences.

Authors
  • Iida, Kei
  • Seki, Motoaki
  • Sakurai, Tetsuya
  • Satou, Masakazu
  • Akiyama, Kenji
  • Toyoda, Tetsuro
  • Konagaya, Akihiko
  • Shinozaki, Kazuo
Type
Published Article
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Publication Date
Jan 01, 2004
Volume
32
Issue
17
Pages
5096–5103
Identifiers
PMID: 15452276
Source
Medline
License
Unknown

Abstract

We mapped RIKEN Arabidopsis full-length (RAFL) cDNAs to the Arabidopsis thaliana genome to search for alternative splicing events. We used 278,734 full-length and 3'/5' terminal reads of the sequences of 220,214 RAFL cDNA clones for the analysis. Eighty-nine percent of the cDNA sequences could be mapped to the genome and were clustered in 17,130 transcription units (TUs). Alternative splicing events were found in 1764 out of 15,214 TUs (11.6%) with multiple sequences. We collected full-length cDNA clones from plants grown under various environmental conditions or from various organs. We then analyzed the correlation between alternative splicing events and environmental stress conditions. Alternative splicing profiles changed according to environmental stress conditions and the various developmental stages of plant organs. In particular, cold-stress conditions affected alternative splicing profiles. The change in alternative splicing profiles under cold stress may be mediated by alternative splicing and transcriptional regulation of splicing factors.

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