Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 28 (1), 193-6

UTRdb and UTRsite: Specialized Databases of Sequences and Functional Elements of 5' and 3' Untranslated Regions of Eukaryotic mRNAs

Affiliations

UTRdb and UTRsite: Specialized Databases of Sequences and Functional Elements of 5' and 3' Untranslated Regions of Eukaryotic mRNAs

G Pesole et al. Nucleic Acids Res.

Abstract

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, a specialized database of 5' and 3' untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRH ome/

Figures

Figure 1
Figure 1
Sample entry of UTRdb. Specialized information not present in the primary EMBL/GenBank database is shown in bold case with active crosslinks with other databases underlined. The ‘UT’ line reports information about completeness or not of the relevant UTR entry (e.g. complete or partial) as well as the number of spanned exons in the case of genomic DNA sequences. The presence in this sequence entry of a ‘5′ribosomal mRNA TOP’ (32–34) (UTRsite entry: U0010) and of a microsatellite element has also been annotated.
Figure 2
Figure 2
Sample entry of UTRsite describing the ‘iron responsive element (IRE)’ (23). The IRE functional pattern which consists of both primary and secondary structure information is described in the ‘Pattern’ section according to the format adopted by the PATSCAN program (http://bio-www.ba.cnr.it:8000/BioWWW/patscanGCG.html ).

Similar articles

See all similar articles

Cited by 28 PubMed Central articles

See all "Cited by" articles

Publication types

LinkOut - more resources

Feedback