untranslated regions


Summary: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.

Top Publications

  1. Haas B, Delcher A, Mount S, Wortman J, Smith R, Hannick L, et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003;31:5654-66 pubmed
    ..The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations. ..
  2. Lee M, Yang R, Gong D, Fried S. Feeding and insulin increase leptin translation. Importance of the leptin mRNA untranslated regions. J Biol Chem. 2007;282:72-80 pubmed
    ..Our data suggest that insulin derepresses leptin translation by a mechanism that requires both the 5'-UTR and the 3'-UTR and may contribute to the increase in leptin production with feeding. ..
  3. Waltering K, Wallén M, Tammela T, Vessella R, Visakorpi T. Mutation screening of the androgen receptor promoter and untranslated regions in prostate cancer. Prostate. 2006;66:1585-91 pubmed
    ..ablation-resistant prostate cancer remain unknown and could include genetic alterations in the promoter or untranslated regions (UTR) of the AR gene...
  4. Lang K, Rieder R, Micura R. Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach. Nucleic Acids Res. 2007;35:5370-8 pubmed
  5. Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, et al. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res. 2010;38:5075-87 pubmed publisher
    ..afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons and upstream open reading frames, which provide remarkable insight ..
  6. Park S, Chung P, Juntawong P, Bailey Serres J, Kim Y, Jung H, et al. Posttranscriptional control of photosynthetic mRNA decay under stress conditions requires 3' and 5' untranslated regions and correlates with differential polysome association in rice. Plant Physiol. 2012;159:1111-24 pubmed publisher
    ..combinations of the mRNA components were analyzed under stress conditions, revealing that both 3' and 5' untranslated regions are necessary for SMD...
  7. Lareau L, Green R, Bhatnagar R, Brenner S. The evolving roles of alternative splicing. Curr Opin Struct Biol. 2004;14:273-82 pubmed
    ..Evolutionary conservation of splicing patterns suggests functional importance and provides insight into the evolutionary history of alternative splicing. ..
  8. Hogan D, Riordan D, Gerber A, Herschlag D, Brown P. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol. 2008;6:e255 pubmed publisher
    ..elements were diverse in sequence, structure, and location: some were found predominantly in 3'-untranslated regions, others in 5'-untranslated regions, some in coding sequences, and many in two or more of these features...
  9. Ptushkina M, Malys N, McCarthy J. eIF4E isoform 2 in Schizosaccharomyces pombe is a novel stress-response factor. EMBO Rep. 2004;5:311-6 pubmed
    ..pombe ribosomes to translate mRNAs with structured leaders in vivo. The tif452 promoter has putative stress-response (T-rich) motifs, whereas elF4E2 seems to be a new type of stress-response factor. ..

More Information


  1. Spence J. Pathway prediction by bioinformatic analysis of the untranslated regions of the CFTR mRNA. Genomics. 2009;94:39-47 pubmed publisher
    Mining the information contained within the genetic code in untranslated regions has proven difficult because of the ambiguity of microRNA and protein binding sites...
  2. Banerjee A, Lin T, Hannapel D. Untranslated regions of a mobile transcript mediate RNA metabolism. Plant Physiol. 2009;151:1831-43 pubmed publisher
    ..of RNA originates in leaf veins and petioles and is induced by a short-day photoperiod, regulated by the untranslated regions, and correlated with enhanced tuber production...
  3. Karlsen M, Villoing S, Rimstad E, Nylund A. Characterization of untranslated regions of the salmonid alphavirus 3 (SAV3) genome and construction of a SAV3 based replicon. Virol J. 2009;6:173 pubmed publisher
    ..Here we report the cloning and characterization of the 5'- and 3'- untranslated regions (UTR) of a SAV3 isolated from Atlantic salmon in Norway...
  4. Elmer K, Fan S, Gunter H, Jones J, Boekhoff S, Kuraku S, et al. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Mol Ecol. 2010;19 Suppl 1:197-211 pubmed publisher
    ..Based on Ks ratios and p-distances between 3'-untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome-..
  5. Toledo Arana A, Dussurget O, Nikitas G, Sesto N, Guet Revillet H, Balestrino D, et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature. 2009;459:950-6 pubmed publisher
    ..mice, we have identified antisense RNAs covering several open-reading frames and long overlapping 5' and 3' untranslated regions. We discovered that riboswitches can act as terminators for upstream genes...
  6. Friebe P, Harris E. Interplay of RNA elements in the dengue virus 5' and 3' ends required for viral RNA replication. J Virol. 2010;84:6103-18 pubmed publisher
    ..We also show that the UAR, DAR, cHP, and CS must act in concert and therefore likely function together to form the tertiary RNA structure of the circularized DENV genome. ..
  7. Kapoor A, Simmonds P, Lipkin W, Zaidi S, Delwart E. Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses. J Virol. 2010;84:10322-8 pubmed publisher
    ..As metagenomic analyses of different environments and organisms continue to yield highly divergent viral genomes NCA provides a rapid and robust method to identify their likely cellular hosts. ..
  8. Roy S, Penny D, Neafsey D. Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol Biol Evol. 2007;24:1140-8 pubmed
    Despite significant progress, the general functional and evolutionary significance of the untranslated regions (UTRs) of eukaryotic transcripts remain mysterious...
  9. Walden W, Selezneva A, Dupuy J, Volbeda A, Fontecilla Camps J, Theil E, et al. Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA. Science. 2006;314:1903-8 pubmed
    ..Extensive conformational changes related to binding the IRE or an iron-sulfur cluster explain the alternate functions of IRP1 as an mRNA regulator or enzyme. ..
  10. Yan Y, Rout S, Kim S, Samal S. Role of untranslated regions of the hemagglutinin-neuraminidase gene in replication and pathogenicity of newcastle disease virus. J Virol. 2009;83:5943-6 pubmed publisher
    To determine the role of untranslated regions (UTRs) in replication and pathogenesis of Newcastle disease virus (NDV), we generated recombinant viruses with deletions in 5' and 3' UTRs of the HN mRNA...
  11. Huang H, Chien C, Jen K, Huang H. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 2006;34:W429-34 pubmed
    ..An intuitive user interface is designed to facilitate the comprehensive annotation of user-submitted mRNA sequences. The RegRNA web server is now available at http://RegRNA.mbc.NCTU.edu.tw/. ..
  12. Sztuba Solińska J, Teramoto T, Rausch J, Shapiro B, Padmanabhan R, Le Grice S. Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome. Nucleic Acids Res. 2013;41:5075-89 pubmed publisher
    ..In addition, our studies targeting elements of the 3' DB and its complementary region PK1 indicated that communication between 5'-3' terminal regions strongly depends on structure and sequence composition of the 5' cyclization region. ..
  13. Langley C, Stevens K, Cardeno C, Lee Y, Schrider D, Pool J, et al. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 2012;192:533-98 pubmed publisher
    ..Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species...
  14. Mykowska A, Sobczak K, Wojciechowska M, Kozlowski P, Krzyzosiak W. CAG repeats mimic CUG repeats in the misregulation of alternative splicing. Nucleic Acids Res. 2011;39:8938-51 pubmed publisher
    ..We propose that alternative splicing misregulation by mutant CAG repeats may contribute to the pathological features of polyglutamine disorders...
  15. VanDongen A, VanDongen H. Effects of mRNA untranslated regions on translational efficiency of NMDA receptor subunits. Neurosignals. 2004;13:194-206 pubmed
    ..One advantage of this level of control is that new receptors can be generated both rapidly and locally in response to appropriate synaptic activity patterns. ..
  16. Kok C, Phuektes P, Bek E, McMinn P. Modification of the untranslated regions of human enterovirus 71 impairs growth in a cell-specific manner. J Virol. 2012;86:542-52 pubmed publisher
    ..Studies of related enteroviruses have indicated that the untranslated regions (UTRs), which control virus-directed translation and replication, also exert significant influence on ..
  17. Takeda M, Ohno S, Seki F, Nakatsu Y, Tahara M, Yanagi Y. Long untranslated regions of the measles virus M and F genes control virus replication and cytopathogenicity. J Virol. 2005;79:14346-54 pubmed
    ..One feature of the moribillivirus genomes is that the M and F genes have long untranslated regions (UTRs). The M and F mRNAs of MeV have 426-nucleotide-long 3' and 583-nucleotide-long 5' UTRs, respectively...
  18. Andolfatto P. Adaptive evolution of non-coding DNA in Drosophila. Nature. 2005;437:1149-52 pubmed
    ..These results imply that, although positive selection is clearly an important facet of protein evolution, adaptive changes to non-coding DNA might have been considerably more common in the evolution of D. melanogaster. ..
  19. Galtier N, Bazin E, Bierne N. GC-biased segregation of noncoding polymorphisms in Drosophila. Genetics. 2006;172:221-8 pubmed
    ..These results, together with previous reports, suggest that GC-biased gene conversion has influenced base composition evolution in Drosophila and explain the correlation between intron and exon GC content. ..
  20. Langat D, Morales P, Fazleabas A, Hunt J. Potential regulatory sequences in the untranslated regions of the baboon MHC class Ib gene, Paan-AG, more closely resemble those in the human MHC class Ia genes than those in the class Ib gene, HLA-G. Immunogenetics. 2004;56:657-66 pubmed
    ..elements controlling expression of Paan-AG resemble those of HLA-A or HLA-G, we cloned the 5' and 3' untranslated regions of Paan-AG...
  21. Patel M, Corey A, Yin L, Ali S, Taylor W, Berry J. Untranslated regions from C4 amaranth AhRbcS1 mRNAs confer translational enhancement and preferential bundle sheath cell expression in transgenic C4 Flaveria bidentis. Plant Physiol. 2004;136:3550-61 pubmed
    ..To determine if RbcS mRNA untranslated regions (UTRs) in themselves could confer any characteristic C4 expression patterns, 5'- and 3'-UTRs of AhRbcS1 ..
  22. Kim D, Kim T, Walsh T, Kobayashi Y, Matise T, Buyske S, et al. Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res. 2004;14:1719-25 pubmed
    ..Therefore, Alu-associated RNA editing may be a mechanism for marking nonstandard transcripts, not destined for translation. ..
  23. Russell K, Hasenkamp S, Emes R, Horrocks P. Analysis of the spatial and temporal arrangement of transcripts over intergenic regions in the human malarial parasite Plasmodium falciparum. BMC Genomics. 2013;14:267 pubmed publisher
  24. Furuse Y, Oshitani H. Evolution of the influenza A virus untranslated regions. Infect Genet Evol. 2011;11:1150-4 pubmed publisher
    In case of the influenza virus, untranslated regions are considered to possess plural functions...
  25. Tuller T, Ruppin E, Kupiec M. Properties of untranslated regions of the S. cerevisiae genome. BMC Genomics. 2009;10:391 pubmed publisher
    ..In this work we perform the first large scale analysis of the length distribution of untranslated regions (promoters, 5' and 3' untranslated regions, terminators) in the genome of the yeast Saccharomyces ..
  26. Master A, Wojcicka A, Piekiełko Witkowska A, Bogusławska J, Popławski P, Tanski Z, et al. Untranslated regions of thyroid hormone receptor beta 1 mRNA are impaired in human clear cell renal cell carcinoma. Biochim Biophys Acta. 2010;1802:995-1005 pubmed publisher
    ..Translational control mediated by untranslated regions (UTRs) regulates cell proliferation, metabolism and responses to cellular stress, processes that are ..
  27. Halvorsen M, Martin J, Broadaway S, Laederach A. Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet. 2010;6:e1001074 pubmed publisher
    ..Single Nucleotide Polymorphisms (SNPs) from the Human Gene Mutation Database (HGMD) that map to the untranslated regions (UTRs) of a gene. Rather than using minimum free energy approaches (e.g...
  28. Lopez E, Viart V, Guittard C, Templin C, René C, Méchin D, et al. Variants in CFTR untranslated regions are associated with congenital bilateral absence of the vas deferens. J Med Genet. 2011;48:152-9 pubmed publisher
    ..Despite extensive testing for point mutations and large rearrangements, a small proportion of alleles still remains unidentified in CBAVD patients...
  29. Chien H, Liao C, Lin Y. FUSE binding protein 1 interacts with untranslated regions of Japanese encephalitis virus RNA and negatively regulates viral replication. J Virol. 2011;85:4698-706 pubmed publisher
    The untranslated regions (UTRs) located at the 5' and 3' ends of the Japanese encephalitis virus (JEV) genome, a positive-sense RNA, are involved in viral translation, the initiation of RNA synthesis, and the packaging of nascent virions...
  30. Baldo L, Santos M, Salzburger W. Comparative transcriptomics of Eastern African cichlid fishes shows signs of positive selection and a large contribution of untranslated regions to genetic diversity. Genome Biol Evol. 2011;3:443-55 pubmed publisher
    ..33% for annotated sequences only including untranslated regions, and decreases to nearly half, 0...
  31. Baricevic M, Forcic D, Santak M, Mazuran R. A comparison of complete untranslated regions of measles virus genomes derived from wild-type viruses and SSPE brain tissues. Virus Genes. 2007;35:17-27 pubmed
    We compared complete untranslated regions (UTRs) of two subacute sclerosing panencephalitis (SSPE) measles virus (MV) strains and two wild-type (wt) MV strains, all belonging to the same genotype (D6)...
  32. Mulhbacher J, Lafontaine D. Ligand recognition determinants of guanine riboswitches. Nucleic Acids Res. 2007;35:5568-80 pubmed
    ..These studies suggest that core variations of guanine aptamers are used to produce a spectrum of ligand binding affinities which is used in vivo by host riboswitches to perform gene regulation. ..
  33. Aouacheria A, Navratil V, López Pérez R, Gutierrez N, Churkin A, Barash D, et al. In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions. BMC Genomics. 2007;8:2 pubmed
    ..to affect gene function, no systematic attention has been paid so far to the changes that occur in untranslated regions of mRNA...
  34. Christoffels A, Bartfai R, Srinivasan H, Komen H, Orban L. Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics. 2006;7 Suppl 5:S2 pubmed
    ..We highlight the need for integrated resources to leverage the wealth of fragmented genomic data. ..
  35. Rentmeister A, Mayer G, Kuhn N, Famulok M. Conformational changes in the expression domain of the Escherichia coli thiM riboswitch. Nucleic Acids Res. 2007;35:3713-22 pubmed
    ..Furthermore, structural probing provides an explanation for the lack of genetic control exerted by a riboswitch variant with mutations in the expression domain that still binds TPP. ..
  36. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008;320:1344-9 pubmed publisher
    The identification of untranslated regions, introns, and coding regions within an organism remains challenging...
  37. Li Y, Korol A, Fahima T, Nevo E. Microsatellites within genes: structure, function, and evolution. Mol Biol Evol. 2004;21:991-1007 pubmed
    ..or simple sequence repeats (SSRs) have been found and characterized within protein-coding genes and their untranslated regions (UTRs). These data provide useful information to study possible SSR functions...
  38. Mazel Sanchez B, Elliott R. Attenuation of bunyamwera orthobunyavirus replication by targeted mutagenesis of genomic untranslated regions and creation of viable viruses with minimal genome segments. J Virol. 2012;86:13672-8 pubmed publisher
    ..BUNV has a tripartite, negative-sense RNA genome. The coding region of each segment is flanked by untranslated regions (UTRs) that are partially complementary...
  39. Zick A, Onn I, Bezalel R, Margalit H, Shlomai J. Assigning functions to genes: identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements. Nucleic Acids Res. 2005;33:4235-42 pubmed
    ..It is suggested that screening for post-transcriptional control elements associated with a specific function provides an efficient method for assigning functions to trypanosomatid genes...
  40. Hong X, Scofield D, Lynch M. Intron size, abundance, and distribution within untranslated regions of genes. Mol Biol Evol. 2006;23:2392-404 pubmed
    ..has largely considered introns within coding sequences (CDSs), without regard for introns located within untranslated regions (UTRs) of genes...
  41. Li M, Wang I, Li Y, Bruzel A, Richards A, Toung J, et al. Widespread RNA and DNA sequence differences in the human transcriptome. Science. 2011;333:53-8 pubmed publisher
    ..These widespread RNA-DNA differences in the human transcriptome provide a yet unexplored aspect of genome variation. ..
  42. Suga K, Welch D, Tanaka Y, Sakakura Y, Hagiwara A. Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. PLoS ONE. 2007;2:e671 pubmed
    ..However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking...
  43. Heinold A, Bauer M, Scherer S, Opelz G, Tran T. Characterization of a new HLA-B allele, HLA-B*5312, and re-evaluation of the published sequences of the untranslated regions of HLA-B*35 and HLA-B*53. Tissue Antigens. 2007;70:319-23 pubmed
    ..According to our sequencing results, HLA-B*5312 resembles HLA-B*350101 regarding its sequence of the untranslated regions. HLA-B*5312 may have been the result of a double crossing over event during which HLA-B*350101 adopted a ..
  44. Barichievy S, Saayman S, von Eije K, Morris K, Arbuthnot P, Weinberg M. The inhibitory efficacy of RNA POL III-expressed long hairpin RNAs targeted to untranslated regions of the HIV-1 5' long terminal repeat. Oligonucleotides. 2007;17:419-31 pubmed
    ..Although lhRNAs themselves require further manipulation to improve their overall efficacy in generating multiple functioning siRNAs, they may prove useful in any combinatorial-based approach to treating HIV-1 infection. ..
  45. Kim S, Samal S. Role of untranslated regions in regulation of gene expression, replication, and pathogenicity of Newcastle disease virus expressing green fluorescent protein. J Virol. 2010;84:2629-34 pubmed publisher
    To gain insight into the role of untranslated regions (UTRs) in regulation of foreign gene expression, replication, and pathogenicity of Newcastle disease virus (NDV), a green fluorescent protein (GFP) gene flanked by 5' and 3' UTRs of ..
  46. Farley B, Pagano J, Ryder S. RNA target specificity of the embryonic cell fate determinant POS-1. RNA. 2008;14:2685-97 pubmed publisher
    ..The results enable prediction of novel targets that explain the pleiotropy of the pos-1 phenotype. ..
  47. Hurowitz E, Drori I, Stodden V, Donoho D, Brown P. Virtual Northern analysis of the human genome. PLoS ONE. 2007;2:e460 pubmed
    ..Some functional classes of protein are encoded by mRNAs whose untranslated regions (UTRs) tend to be longer or shorter than average; these functional classes were similar in both human and ..
  48. Chen N, Stein L. Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. Genome Res. 2006;16:606-17 pubmed
  49. Jacobs G, Stockwell P, Tate W, Brown C. Transterm--extended search facilities and improved integration with other databases. Nucleic Acids Res. 2006;34:D37-40 pubmed
    ..Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at http://uther.otago.ac.nz/Transterm.html. ..
  50. Elemento O, Slonim N, Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell. 2007;28:337-50 pubmed
  51. Pfeffer S, Zavolan M, Grässer F, Chien M, Russo J, Ju J, et al. Identification of virus-encoded microRNAs. Science. 2004;304:734-6 pubmed
    ..Given that miRNAs function in RNA silencing pathways either by targeting messenger RNAs for degradation or by repressing translation, we identified viral regulators of host and/or viral gene expression. ..
  52. Khaladkar M, Liu J, Wen D, Wang J, Tian B. Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment. BMC Genomics. 2008;9:189 pubmed publisher
    b>UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability...
  53. Pesole G, Liuni S, Grillo G, Licciulli F, Larizza A, Makalowski W, et al. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2000;28:193-6 pubmed
    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...