Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1999 Jan 1;27(1):188–191. doi: 10.1093/nar/27.1.188

UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs.

G Pesole 1, S Liuni 1, G Grillo 1, M Ippedico 1, A Larizza 1, W Makalowski 1, C Saccone 1
PMCID: PMC148131  PMID: 9847176

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 (http://bigarea.area.ba.cnr.it:8000/BioWWW/#U TRdb), 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.

Full Text

The Full Text of this article is available as a PDF (81.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Beelman C. A., Parker R. Degradation of mRNA in eukaryotes. Cell. 1995 Apr 21;81(2):179–183. doi: 10.1016/0092-8674(95)90326-7. [DOI] [PubMed] [Google Scholar]
  2. Chen C. Y., Shyu A. B. AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem Sci. 1995 Nov;20(11):465–470. doi: 10.1016/s0968-0004(00)89102-1. [DOI] [PubMed] [Google Scholar]
  3. Curtis D., Lehmann R., Zamore P. D. Translational regulation in development. Cell. 1995 Apr 21;81(2):171–178. doi: 10.1016/0092-8674(95)90325-9. [DOI] [PubMed] [Google Scholar]
  4. Dahanukar A., Wharton R. P. The Nanos gradient in Drosophila embryos is generated by translational regulation. Genes Dev. 1996 Oct 15;10(20):2610–2620. doi: 10.1101/gad.10.20.2610. [DOI] [PubMed] [Google Scholar]
  5. Decker C. J., Parker R. Mechanisms of mRNA degradation in eukaryotes. Trends Biochem Sci. 1994 Aug;19(8):336–340. doi: 10.1016/0968-0004(94)90073-6. [DOI] [PubMed] [Google Scholar]
  6. Dsouza M., Larsen N., Overbeek R. Searching for patterns in genomic data. Trends Genet. 1997 Dec;13(12):497–498. doi: 10.1016/s0168-9525(97)01347-4. [DOI] [PubMed] [Google Scholar]
  7. Goodwin E. B., Okkema P. G., Evans T. C., Kimble J. Translational regulation of tra-2 by its 3' untranslated region controls sexual identity in C. elegans. Cell. 1993 Oct 22;75(2):329–339. doi: 10.1016/0092-8674(93)80074-o. [DOI] [PubMed] [Google Scholar]
  8. Grillo G., Attimonelli M., Liuni S., Pesole G. CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. Comput Appl Biosci. 1996 Feb;12(1):1–8. doi: 10.1093/bioinformatics/12.1.1. [DOI] [PubMed] [Google Scholar]
  9. Hentze M. W., Kühn L. C. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8175–8182. doi: 10.1073/pnas.93.16.8175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hubert N., Walczak R., Sturchler C., Myslinski E., Schuster C., Westhof E., Carbon P., Krol A. RNAs mediating cotranslational insertion of selenocysteine in eukaryotic selenoproteins. Biochimie. 1996;78(7):590–596. doi: 10.1016/s0300-9084(96)80005-8. [DOI] [PubMed] [Google Scholar]
  11. Jurka J. Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol. 1998 Jun;8(3):333–337. doi: 10.1016/s0959-440x(98)80067-5. [DOI] [PubMed] [Google Scholar]
  12. Kaufman R. J. Control of gene expression at the level of translation initiation. Curr Opin Biotechnol. 1994 Oct;5(5):550–557. doi: 10.1016/0958-1669(94)90073-6. [DOI] [PubMed] [Google Scholar]
  13. Klausner R. D., Rouault T. A., Harford J. B. Regulating the fate of mRNA: the control of cellular iron metabolism. Cell. 1993 Jan 15;72(1):19–28. doi: 10.1016/0092-8674(93)90046-s. [DOI] [PubMed] [Google Scholar]
  14. Makałowski W., Zhang J., Boguski M. S. Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res. 1996 Sep;6(9):846–857. doi: 10.1101/gr.6.9.846. [DOI] [PubMed] [Google Scholar]
  15. McCarthy J. E., Kollmus H. Cytoplasmic mRNA-protein interactions in eukaryotic gene expression. Trends Biochem Sci. 1995 May;20(5):191–197. doi: 10.1016/s0968-0004(00)89006-4. [DOI] [PubMed] [Google Scholar]
  16. Mengeritsky G., Smith T. F. Recognition of characteristic patterns in sets of functionally equivalent DNA sequences. Comput Appl Biosci. 1987 Sep;3(3):223–227. doi: 10.1093/bioinformatics/3.3.223. [DOI] [PubMed] [Google Scholar]
  17. Ostareck-Lederer A., Ostareck D. H., Standart N., Thiele B. J. Translation of 15-lipoxygenase mRNA is inhibited by a protein that binds to a repeated sequence in the 3' untranslated region. EMBO J. 1994 Mar 15;13(6):1476–1481. doi: 10.1002/j.1460-2075.1994.tb06402.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Pesole G., Fiormarino G., Saccone C. Sequence analysis and compositional properties of untranslated regions of human mRNAs. Gene. 1994 Mar 25;140(2):219–225. doi: 10.1016/0378-1119(94)90547-9. [DOI] [PubMed] [Google Scholar]
  19. Pesole G., Grillo G., Liuni S. Databases of mRNA untranslated regions for metazoa. Comput Chem. 1996 Mar;20(1):141–144. doi: 10.1016/s0097-8485(96)80016-7. [DOI] [PubMed] [Google Scholar]
  20. Pesole G., Liuni S., Grillo G., Saccone C. Structural and compositional features of untranslated regions of eukaryotic mRNAs. Gene. 1997 Dec 31;205(1-2):95–102. doi: 10.1016/s0378-1119(97)00407-1. [DOI] [PubMed] [Google Scholar]
  21. Singer R. H. The cytoskeleton and mRNA localization. Curr Opin Cell Biol. 1992 Feb;4(1):15–19. doi: 10.1016/0955-0674(92)90053-f. [DOI] [PubMed] [Google Scholar]
  22. Sonenberg N. mRNA translation: influence of the 5' and 3' untranslated regions. Curr Opin Genet Dev. 1994 Apr;4(2):310–315. doi: 10.1016/s0959-437x(05)80059-0. [DOI] [PubMed] [Google Scholar]
  23. St Johnston D. The intracellular localization of messenger RNAs. Cell. 1995 Apr 21;81(2):161–170. doi: 10.1016/0092-8674(95)90324-0. [DOI] [PubMed] [Google Scholar]
  24. Verrotti A. C., Thompson S. R., Wreden C., Strickland S., Wickens M. Evolutionary conservation of sequence elements controlling cytoplasmic polyadenylylation. Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):9027–9032. doi: 10.1073/pnas.93.17.9027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Walczak R., Westhof E., Carbon P., Krol A. A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs. RNA. 1996 Apr;2(4):367–379. [PMC free article] [PubMed] [Google Scholar]
  26. Wilhelm J. E., Vale R. D. RNA on the move: the mRNA localization pathway. J Cell Biol. 1993 Oct;123(2):269–274. doi: 10.1083/jcb.123.2.269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Williams A. S., Marzluff W. F. The sequence of the stem and flanking sequences at the 3' end of histone mRNA are critical determinants for the binding of the stem-loop binding protein. Nucleic Acids Res. 1995 Feb 25;23(4):654–662. doi: 10.1093/nar/23.4.654. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Zaidi S. H., Malter J. S. Amyloid precursor protein mRNA stability is controlled by a 29-base element in the 3'-untranslated region. J Biol Chem. 1994 Sep 30;269(39):24007–24013. [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES