RT Journal
A1 Zavolan, Mihaela
A1 Kondo, Shinji
A1 Schönbach, Christian
A1 Adachi, Jun
A1 Hume, David A.
A1 RIKEN GER Group
A1 GSL Members
A1 Hayashizaki, Yoshihide
A1 Gaasterland, Terry
T1 Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome
JF Genome Research 
JO Genome Research 
YR 2003 
FD June 01 
VO 13 
IS 6b 
SP 1290 
OP 1300 
DO 10.1101/gr.1017303 
UL http://genome.cshlp.org/content/13/6b/1290.abstract 
AB 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 nucleotide distributions around their splice  junctions, and the frequencies of occurrence of several short sequence  motifs.