Home LiteratureArticle Details
PMID: 10592223 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs.

Nucleic acids research ·Vol. 28 ·No. 1 ·2000-01-01 ·Pages 193-6

Pesole G, Liuni S, Grillo G, Licciulli F, Larizza A, Makalowski W, Saccone C

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/

MeSH Terms
3' Untranslated Regions 5' Untranslated Regions Base Sequence Databases, Factual Eukaryotic Cells Internet Molecular Sequence Data RNA, Messenger/genetics Regulatory Sequences, Nucleic Acid Untranslated Regions
Chemicals
3' Untranslated Regions 5' Untranslated Regions RNA, Messenger Untranslated Regions
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Pesole G
Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, via Celoria 26, 20133 Milano, Italy. [email protected]
Liuni S
Grillo G
Licciulli F
Larizza A
Makalowski W
Saccone C
References (37)
37 references, click to expand
  1. Recognition of characteristic patterns in sets of functionally equivalent DNA sequences.
    Comput Appl Biosci. 1987 Sep;3(3):223-7 PMID: 3330960
  2. It's a knockout!
    Trends Genet. 1999 Sep;15(9):379-80 PMID: 10461208
  3. The cytoskeleton and mRNA localization.
    Curr Opin Cell Biol. 1992 Feb;4(1):15-9 PMID: 1558749
  4. Regulating the fate of mRNA: the control of cellular iron metabolism.
    Cell. 1993 Jan 15;72(1):19-28 PMID: 8380757
  5. Polypyrimidine tracts and their binding proteins: regulatory sites for posttranscriptional modulation of gene expression.
    Biochemistry. 1993 Mar 30;32(12):2931-7 PMID: 8457557
  6. Translational regulation of tra-2 by its 3' untranslated region controls sexual identity in C. elegans.
    Cell. 1993 Oct 22;75(2):329-39 PMID: 8402916
  7. RNA on the move: the mRNA localization pathway.
    J Cell Biol. 1993 Oct;123(2):269-74 PMID: 8408211
  8. 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):1476-81 PMID: 8137829
  9. Sequence analysis and compositional properties of untranslated regions of human mRNAs.
    Gene. 1994 Mar 25;140(2):219-25 PMID: 8144029
  10. mRNA translation: influence of the 5' and 3' untranslated regions.
    Curr Opin Genet Dev. 1994 Apr;4(2):310-5 PMID: 8032210
  11. 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):24007-13 PMID: 7929051
  12. Mechanisms of mRNA degradation in eukaryotes.
    Trends Biochem Sci. 1994 Aug;19(8):336-40 PMID: 7940679
  13. Control of gene expression at the level of translation initiation.
    Curr Opin Biotechnol. 1994 Oct;5(5):550-7 PMID: 7765472
  14. 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):654-62 PMID: 7899087
  15. The intracellular localization of messenger RNAs.
    Cell. 1995 Apr 21;81(2):161-70 PMID: 7736568
  16. Translational regulation in development.
    Cell. 1995 Apr 21;81(2):171-8 PMID: 7736569
  17. Degradation of mRNA in eukaryotes.
    Cell. 1995 Apr 21;81(2):179-83 PMID: 7736570
  18. Cytoplasmic mRNA-protein interactions in eukaryotic gene expression.
    Trends Biochem Sci. 1995 May;20(5):191-7 PMID: 7610483
  19. AU-rich elements: characterization and importance in mRNA degradation.
    Trends Biochem Sci. 1995 Nov;20(11):465-70 PMID: 8578590
  20. A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs.
    RNA. 1996 Apr;2(4):367-79 PMID: 8634917
  21. CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases.
    Comput Appl Biosci. 1996 Feb;12(1):1-8 PMID: 8670613
  22. 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):8175-82 PMID: 8710843
  23. SRS: information retrieval system for molecular biology data banks.
    Methods Enzymol. 1996;266:114-28 PMID: 8743681
  24. Evolutionary conservation of sequence elements controlling cytoplasmic polyadenylylation.
    Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):9027-32 PMID: 8799148
  25. Databases of mRNA untranslated regions for metazoa.
    Comput Chem. 1996 Mar;20(1):141-4 PMID: 8867845
  26. Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences.
    Genome Res. 1996 Sep;6(9):846-57 PMID: 8889551
  27. The Nanos gradient in Drosophila embryos is generated by translational regulation.
    Genes Dev. 1996 Oct 15;10(20):2610-20 PMID: 8895662
  28. RNAs mediating cotranslational insertion of selenocysteine in eukaryotic selenoproteins.
    Biochimie. 1996;78(7):590-6 PMID: 8955902
  29. TOP genes: a translationally controlled class of genes including those coding for ribosomal proteins.
    Prog Mol Subcell Biol. 1997;18:1-17 PMID: 8994258
  30. RNA-protein interactions within the 3 ' untranslated region of vimentin mRNA.
    Nucleic Acids Res. 1997 Aug 15;25(16):3362-70 PMID: 9241253
  31. Searching for patterns in genomic data.
    Trends Genet. 1997 Dec;13(12):497-8 PMID: 9433140
  32. Structural and compositional features of untranslated regions of eukaryotic mRNAs.
    Gene. 1997 Dec 31;205(1-2):95-102 PMID: 9461382
  33. Characterization of the RNA binding proteins forming complexes with a novel putative regulatory region in the 3'-UTR of TNF-alpha mRNA.
    Nucleic Acids Res. 1998 Jun 1;26(11):2803-12 PMID: 9592171
  34. Repeats in genomic DNA: mining and meaning.
    Curr Opin Struct Biol. 1998 Jun;8(3):333-7 PMID: 9666329
  35. Ten nucleotide cis element in the 3'-untranslated region of the GLUT1 glucose transporter mRNA increases gene expression via mRNA stabilization.
    Brain Res Mol Brain Res. 1998 Aug 15;59(1):109-13 PMID: 9729315
  36. RNA localization in development.
    Annu Rev Biochem. 1998;67:335-94 PMID: 9759492
  37. A regulatory cis element and a specific binding factor involved in the mitogenic control of murine ribosomal protein L32 translation.
    J Biol Chem. 1992 Jan 5;267(1):508-14 PMID: 1309750
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/28.1.193
Email
[email protected]
Published
2000-01-01
Pages
193-6
Language
English
Region
England
NLM ID
0411011
PMCID
PMC102415
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/28.1.193 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2