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Nucleic Acids Research 2005 33(Database Issue):D141-D146; doi:10.1093/nar/gki021
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Nucleic Acids Research, 2005, Vol. 33, Database issue D141-D146
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

Flavio Mignone1, Giorgio Grillo2, Flavio Licciulli2, Michele Iacono1, Sabino Liuni2, Paul J. Kersey4, Jorge Duarte4, Cecilia Saccone2,3 and Graziano Pesole1,2,*

1 Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, via Celoria 26, 20133 Milano, Italy, 2 Sezione di Bioinformatica e Genomica, Istituto Tecnologie Biomediche del Consiglio Nazionale delle Ricerche (CNR), via Amendola 165/A, 70126 Bari, Italy, 3 Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, via Orabona 4, 70126 Bari, Italy and 4 EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK

* To whom correspondence should be addressed. Tel: +39 02 50314915; Fax: +39 02 50314912; Email: graziano.pesole{at}unimi.it

Received September 15, 2004; Accepted September 18, 2004

The 5' and 3' untranslated regions of eukaryotic mRNAs play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated (and also collated as the UTRsite database) and cross-links to genomic and protein data are provided. The integration of UTRdb with genomic and protein data has allowed the implementation of a powerful retrieval resource for the selection and extraction of UTR subsets based on their genomic coordinates and/or features of the protein encoded by the relevant mRNA (e.g. GO term, PFAM domain, etc.). All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://www.ba.itb.cnr.it/UTR/.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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