Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data.
BACKGROUND
Alternative RNA splicing allows cells to produce multiple protein isoforms from one gene. These isoforms may have specialized functions, and may be tissue- or stage-specific. Our aim was to use computational analysis of SAGE and genomic data to predict alternatively spliced transcripts expressed in C. elegans.


RESULTS
We predicted novel alternatively spliced variants and confirmed five of eighteen candidates selected for experimental validation by RT-PCR tests and DNA sequencing.


CONCLUSIONS
We show that SAGE data can be efficiently used to discover alternative mRNA isoforms, including those with skipped exons or retained introns. Our results also imply that C. elegans may produce a larger number of alternatively spliced transcripts than initially estimated.
Ruzanov
Peter
P
Michael Smith Laboratories University of British Columbia, Vancouver BC V6T 1Z4, Canada. pruzanov@bcgsc.ca
Jones
Steven J
SJ
Riddle
Donald L
DL
D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D019295:Computational Biology; D017931:DNA Primers; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
D017931:DNA Primers; D012333:RNA, Messenger