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Open Access Open Badges Research article

Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data

Peter Ruzanov1, Steven J Jones2 and Donald L Riddle1*

Author Affiliations

1 Michael Smith Laboratories University of British Columbia, Vancouver BC V6T 1Z4, Canada

2 Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC V5Z 4S6, Canada

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BMC Genomics 2007, 8:447  doi:10.1186/1471-2164-8-447

Published: 30 November 2007



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.


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


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.