TRANSCRIPTOME 2002: From Functional Genomics to Systems
UTRDB and UTRSITE: Specialized Databases of Sequences and Functional Elements of 5' and 3' Untranslated Regions of Eukaryotic mRNAs
Pesole, Graziano1, Gissi C.1, Grillo G.2, Licciulli F.2, Mignone F.1, Iacono M.1, Liuni S.2, 1UniversitÓ di Milano, Milan, ITALY, 2 CSMME-C.N.R., Bari, ITALY
The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA nucleo-cytoplasmic transport, subcellular localization, stability and translation efficiency. In order to study the general structural and compositional features of these sequences we have developed UTRdb, a specialized database of 5' and 3' UTR sequences of eukaryotic mRNAs cleaned from redundancy (Pesole, Liuni et al. 2002).UTRdb (release 15.0) contains about 250,000 entries (>65,000,000 nucleotides) which are also annotated for the presence of functional sequence patterns whose biological activity has been experimentally demonstrated. All these patterns have been collected in the UTRsite database where for each functional pattern, corresponding to a specific entry, the consensus structure is reported with a short description of its biological activity and the relevant bibliography. All Web resources we implemented for the retrieval and the analysis of UTR sequences are available at the UTR home page (http://bighost.area.ba.cnr.-it/BIG/UTRHome/) we recently implemented. UTRdb entries can be retrieved through the SRS system where crosslinks to UTRsite as well as to the nucleotide or aminoacid primary database are also established. Through the Web facility UTRscan any input sequence can be searched for the presence of a functional pattern annotated in UTRsite and UTRblast allows to assess sequence similarity between a query sequence and UTRdb entries.The analysis of complete UTR sequences contained in this database allowed us to define specific structural and compositional features of UTRs from mRNAs belonging to various eukaryotic taxa (Pesole, Grillo et al. 2000). Pesole, G., G. Grillo, et al. (2000). 'The untranslated regions of eukaryotic mRNAs: structure, function and bioinformatic tools for their analysis.' Briefings in Bioinformatics 1(3): 236-249.Pesole, G., S. Liuni, et al. (2002). 'UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002.' Nucleic Acids Res 30(1): 335-40.
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