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Nucleic Acids Res. 2007 Jan;35(Database issue):D110-5. Epub 2006 Nov 1.

U12DB: a database of orthologous U12-type spliceosomal introns.

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  • 1Genome Bioinformatics Laboratory, Center for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Spain. talioto@imim.es

Abstract

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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