Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome

Zavolan, M., Kondo, S., Schonbach, C., Adachi, J., Hume, D. A., Hayashizaki, Y., Gaasterland, T., RIKEN GER Grp and GLS Members (2003) Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Research, 13 6B: 1290-1300. doi:10.1101/gr.1017303

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Author Zavolan, M.
Kondo, S.
Schonbach, C.
Adachi, J.
Hume, D. A.
Hayashizaki, Y.
Gaasterland, T.
RIKEN GER Grp
GLS Members
Title Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2003-06-01
Sub-type Article (original research)
DOI 10.1101/gr.1017303
Open Access Status File (Publisher version)
Volume 13
Issue 6B
Start page 1290
End page 1300
Total pages 11
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Press
Collection year 2003
Language eng
Abstract We analyzed the FANTOM2 clone set of 60,770 RIKEN full-length mouse cDNA sequences and 44,122 public mRNA sequences. We developed a new computational procedure to identify and classify the forms of splice variation evident in this data set and organized the results into a publicly accessible database that can be used for future expression array construction, structural genomics, and analyses of the mechanism and regulation of alternative splicing. Statistical analysis shows that at least 41% and possibly as much as 60% of multiexon genes in mouse have multiple splice forms. Of the transcription units with multiple splice forms, 49% contain transcripts in which the apparent use of an alternative transcription start (stop) is accompanied by alternative splicing of the initial (terminal) exon. This implies that alternative transcription may frequently induce alternative splicing. The fact that 73% of all exons with splice variation fall within the annotated coding region indicates that most splice variation is likely to affect the protein form. Finally, we compared the set of constitutive (present in all transcripts) exons with the set of cryptic (present only in some transcripts) exons and found statistically significant differences in their length distributions, the nucleoticle distributions around their splice junctions, and the frequencies of occurrence of several short sequence motifs.
Keyword Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
Full-length Cdnas
Sr Proteins
Site Selection
Human Genome
Human Genes
Hnrnp A1
Exon
Sequence
Intron
Identification
Q-Index Code C1
Institutional Status UQ

 
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Created: Wed, 15 Aug 2007, 02:52:11 EST