UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
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/.
Grillo
Giorgio
G
Istituto Tecnologie Biomediche del Consiglio Nazionale delle Ricerche, via Amendola 122/D, 70126 Bari, Italy.
Turi
Antonio
A
Licciulli
Flavio
F
Mignone
Flavio
F
Liuni
Sabino
S
Banfi
Sandro
S
Gennarino
Vincenzo Alessandro
VA
Horner
David S
DS
Pavesi
Giulio
G
Picardi
Ernesto
E
Pesole
Graziano
G
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D018745:Genome, Plant; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D020033:Protein Isoforms; D012984:Software; D014584:User-Computer Interface
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D020033:Protein Isoforms