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Nucleic Acids Research Advance Access published online on October 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp902
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

Giorgio Grillo1, Antonio Turi2, Flavio Licciulli1, Flavio Mignone3, Sabino Liuni1, Sandro Banfi4, Vincenzo Alessandro Gennarino4, David S. Horner5, Giulio Pavesi5, Ernesto Picardi2 and Graziano Pesole1,2,*

1Istituto Tecnologie Biomediche del Consiglio Nazionale delle Ricerche (CNR), via Amendola 122/D, 70126 Bari, 2Dipartimento di Biochimica e Biologia Molecolare ‘E. Quagliariello’, Università di Bari, via Orabona 4, 70126 Bari, 3Dipartimento di Chimica Strutturale e Stereochimica Inorganica, Università degli Studi di Milano, 20133 Milano, 4Telethon Institute of Genetics and Medicine, via Pietro Castellino 111, 80131 Naples and 5Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, via Celoria 26, 20133 Milano, Italy

*To whom correspondence should be addressed. Tel: +39 080 5443588; Fax; +39 080 5443317; Email: graziano.pesole{at}biologia.uniba.it

Received September 1, 2009. Revised September 29, 2009. Accepted October 6, 2009.

The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) 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 where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. In the current update, the UTR entries have been organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://utrdb.ba.itb.cnr.it/.


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