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Nucleic Acids Research, 2000, Vol. 28, No. 1 91-93
© 2000 Oxford University Press

The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans

W. James Kent and Alan M. Zahler*

Department of Biology and Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA

The Intronerator (http://www.cse.ucsc.edu/~kent/intronerator/ ) is a set of web-based tools for exploring RNA splicing and gene structure in Caenorhabditis elegans. It includes a display of cDNA alignments with the genomic sequence, a catalog of alternatively spliced genes and a database of introns. The cDNA alignments include >100 000 ESTs and almost 1000 full-length cDNAs. ESTs from embryos and mixed stage animals as well as full-length cDNAs can be compared in the alignment display with each other and with predicted genes. The alt-splicing catalog includes 844 open reading frames for which there is evidence of alternative splicing of pre-mRNA. The intron database includes 28 478 introns, and can be searched for patterns near the splice junctions.

* To whom correspondence should be addressed. Tel: +1 831 459 5131; Fax: +1 831 459 3737; Email: zahler@biology.ucsc.edu


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