UTRdb

UTRdb 2.0
Content
Description	sequences and regulatory motifs of untranslated regions of eukaryotic mRNAs
Organisms	Eukaryotes
Contact
Laboratory	Università degli Studi di Bari, Piazza Umberto I, 1, 70121 Bari BA, Italy
Authors	Claudio Lo Giudice
Primary citation	Lo Giudice & al. (2023)
Access
Website	http://utrdb.cloud.ba.infn.it/utrdb/

UTRdb 2.0 is an updated version of the specialized database UTRdb, which focuses on the 5' and 3' untranslated regions (UTRs) of eukaryotic mRNAs. These UTRs play essential roles in the post-transcriptional regulation of gene expression by influencing various processes, including nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization, and mRNA stability. Since its launch in 1996, UTRdb has been a valuable resource for researchers studying UTR sequences and their functional implications.

Content and features

UTRdb 2.0 contains a comprehensive collection of over 26 million entries, derived from more than 6 million genes across 573 species. The database is enriched with a curated set of functional annotations to enhance the understanding of UTR function. These annotations include:

CAGE tags: marking the completeness of 5' UTRs
PolyA signals: indicating the completeness of 3' UTRs
uORFs and IRES: annotating upstream open reading frames (uORFs) and internal ribosome entry sites (IRES) in 5' UTRs
miRNA targets: annotating experimentally validated miRNA targets in 3' UTRs
Evolutionarily conserved blocks: identifying conserved regions across species
Rfam motifs: recognizing RNA motifs associated with function
ADAR-mediated RNA editing: annotating RNA editing events mediated by the ADAR enzyme
m6A modifications: marking mRNA modifications related to N6-methyladenosine

Web interface and access

UTRdb 2.0 provides a flexible web interface that allows users to select and retrieve subsets of UTRs based on various criteria. This tool offers comprehensive download options to access the data for further analysis.

References

1 2 Lo Giudice, Chiara; Zambelli Francesco; Chiara Matteo; Pavesi Giulio; Tangaro Marco Antonio; Picardi Ernesto; Pesole Graziano (Jan 2023). "UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions". Nucleic Acids Res. 51 (D1): D337–D344. doi:10.1093/nar/gkac1016. PMC 9825521. PMID 36399486.
↑ Grillo, Giorgio; Turi Antonio; Licciulli Flavio; Mignone Flavio; Liuni Sabino; Banfi Sandro; Gennarino Vincenzo Alessandro; Horner David S; Pavesi Giulio; Picardi Ernesto; Pesole Graziano (Jan 2010). "UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs". Nucleic Acids Res. 38 (Suppl_1): D75-80. doi:10.1093/nar/gkp902. PMC 2808995. PMID 19880380.

External links

UTRdb

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[pmid36399486-1] 1 2 Lo Giudice, Chiara; Zambelli Francesco; Chiara Matteo; Pavesi Giulio; Tangaro Marco Antonio; Picardi Ernesto; Pesole Graziano (Jan 2023). "UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions". Nucleic Acids Res. 51 (D1): D337–D344. doi:10.1093/nar/gkac1016. PMC 9825521. PMID 36399486.

[pmid19880380-2] Grillo, Giorgio; Turi Antonio; Licciulli Flavio; Mignone Flavio; Liuni Sabino; Banfi Sandro; Gennarino Vincenzo Alessandro; Horner David S; Pavesi Giulio; Picardi Ernesto; Pesole Graziano (Jan 2010). "UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs". Nucleic Acids Res. 38 (Suppl_1): D75-80. doi:10.1093/nar/gkp902. PMC 2808995. PMID 19880380.