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Nucleic Acids Research Advance Access published online on November 1, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl796
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

U12DB: a database of orthologous U12-type spliceosomal introns

Tyler S. Alioto*

Genome Bioinformatics Laboratory, Center for Genomic Regulation Doctor Aiguader 88, 08003 Barcelona, Spain

*To whom correspondence should be addressed. Tel: +34 93 316 0169; Fax: +34 93 396 9983; Email: talioto{at}imim.es

Received August 10, 2006. Revised September 26, 2006. Accepted October 2, 2006.

U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12-type introns of completely sequenced eukaryotic genomes in a framework that groups orthologous introns with each other. This will aid further investigations into the evolution and mechanism of U12-dependent splicing as well as assist ongoing genome annotation efforts. Public access to the U12DB is available at http://genome.imim.es/cgi-bin/u12db/u12db.cgi.


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