consensus sequence

Summary

Summary: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.

Top Publications

  1. pmc Phosphorylation of CBP by IKKalpha promotes cell growth by switching the binding preference of CBP from p53 to NF-kappaB
    Wei Chien Huang
    Department of Pharmacology, College of Medicine, National Taiwan University, Taipei 10018, Taiwan Department of Molecular and Cellular Oncology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Mol Cell 26:75-87. 2007
  2. pmc The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
    Genome Res 19:1316-23. 2009
  3. ncbi Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level
    Corey B Moore
    Centre for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital and Murdoch University, Level 2 North Block, Royal Perth Hospital, Wellington Street, WA 6000, Australia
    Science 296:1439-43. 2002
  4. pmc CD-Search: protein domain annotations on the fly
    Aron Marchler-Bauer
    Computational Biology Branch, NCBI, National Library of Medicine, NIH, Building 38A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:W327-31. 2004
  5. pmc Insights from genomic profiling of transcription factors
    Peggy J Farnham
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Nat Rev Genet 10:605-16. 2009
  6. ncbi The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification
    D A Sampson
    Johns Hopkins University, School of Hygiene and Public Health, Department of Biochemistry and Molecular Biology, Baltimore, Maryland 21205, USA
    J Biol Chem 276:21664-9. 2001
  7. pmc A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
    Riccardo Velasco
    IASMA Research Center, San Michele all Adige, Trento, Italy
    PLoS ONE 2:e1326. 2007
  8. pmc Definition of the bacterial N-glycosylation site consensus sequence
    Michael Kowarik
    Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, Switzerland
    EMBO J 25:1957-66. 2006
  9. pmc The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
    Tomohiro Shimada
    Department of Frontier Bioscience and Micro Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184 8584, Nippon Institute for Biological Science, Ome, Tokyo 198 0024, Japan
    Nucleic Acids Res 36:3950-5. 2008
  10. pmc Identification of a novel Nrf2-regulated antioxidant response element (ARE) in the mouse NAD(P)H:quinone oxidoreductase 1 gene: reassessment of the ARE consensus sequence
    Paul Nioi
    Biomedical Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, Scotland, UK
    Biochem J 374:337-48. 2003

Detail Information

Publications285 found, 100 shown here

  1. pmc Phosphorylation of CBP by IKKalpha promotes cell growth by switching the binding preference of CBP from p53 to NF-kappaB
    Wei Chien Huang
    Department of Pharmacology, College of Medicine, National Taiwan University, Taipei 10018, Taiwan Department of Molecular and Cellular Oncology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Mol Cell 26:75-87. 2007
    ..Our results suggest that phosphorylation of CBP by IKKalpha regulates the CBP-mediated crosstalk between NF-kappaB and p53 and thus may be a critical factor in the promotion of cell proliferation and tumor growth...
  2. pmc The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
    Genome Res 19:1316-23. 2009
    ..The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions...
  3. ncbi Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level
    Corey B Moore
    Centre for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital and Murdoch University, Level 2 North Block, Royal Perth Hospital, Wellington Street, WA 6000, Australia
    Science 296:1439-43. 2002
    ..At a population level, the degree of HLA-associated selection in viral sequence was predictive of viral load. These results support a fundamental role for HLA-restricted immune responses in driving and shaping HIV-1 evolution in vivo...
  4. pmc CD-Search: protein domain annotations on the fly
    Aron Marchler-Bauer
    Computational Biology Branch, NCBI, National Library of Medicine, NIH, Building 38A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:W327-31. 2004
    ..CD-Search can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi...
  5. pmc Insights from genomic profiling of transcription factors
    Peggy J Farnham
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Nat Rev Genet 10:605-16. 2009
    ..It also suggests future experiments that may further our understanding of the causes and consequences of transcription factor-genome interactions...
  6. ncbi The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification
    D A Sampson
    Johns Hopkins University, School of Hygiene and Public Health, Department of Biochemistry and Molecular Biology, Baltimore, Maryland 21205, USA
    J Biol Chem 276:21664-9. 2001
    ..The SUMO-1 consensus sequence (SUMO-1-CS) is a motif of conserved residues surrounding the modified lysine residue of most SUMO-1 ..
  7. pmc A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
    Riccardo Velasco
    IASMA Research Center, San Michele all Adige, Trento, Italy
    PLoS ONE 2:e1326. 2007
    ..In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented...
  8. pmc Definition of the bacterial N-glycosylation site consensus sequence
    Michael Kowarik
    Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, Switzerland
    EMBO J 25:1957-66. 2006
    ..jejuni N-glycoprotein AcrA required for accepting an N-glycan. We found that the eukaryotic primary consensus sequence for N-glycosylation is N terminally extended to D/E-Y-N-X-S/T (Y, X not equalP) for recognition by the ..
  9. pmc The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
    Tomohiro Shimada
    Department of Frontier Bioscience and Micro Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184 8584, Nippon Institute for Biological Science, Ome, Tokyo 198 0024, Japan
    Nucleic Acids Res 36:3950-5. 2008
    ..We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness...
  10. pmc Identification of a novel Nrf2-regulated antioxidant response element (ARE) in the mouse NAD(P)H:quinone oxidoreductase 1 gene: reassessment of the ARE consensus sequence
    Paul Nioi
    Biomedical Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, Scotland, UK
    Biochem J 374:337-48. 2003
    ..A comprehensive mutation study of this ARE revealed that it does not conform to the currently accepted ARE consensus sequence [(5'-TMAnnRTGAYnnnGCRwwww-3', with essential nucleotides shown in capitals); two cytosine residues (shown in ..
  11. pmc Characterization of genome-wide p53-binding sites upon stress response
    Leonie Smeenk
    Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
    Nucleic Acids Res 36:3639-54. 2008
    ..Our study greatly expands the known, experimentally validated p53 binding site repertoire and serves as a valuable knowledgebase for future research...
  12. ncbi Cutting edge: IFN consensus sequence binding protein/IFN regulatory factor 8 drives the development of type I IFN-producing plasmacytoid dendritic cells
    Hideki Tsujimura
    Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    J Immunol 170:1131-5. 2003
    IFN consensus sequence binding protein (ICSBP/IFN regulatory factor 8) is a hematopoietic cell-specific transcription factor essential for the generation of CD8 alpha(+) dendritic cells (DCs)...
  13. pmc Interferon (IFN) consensus sequence-binding protein, a transcription factor of the IFN regulatory factor family, regulates immune responses in vivo through control of interleukin 12 expression
    N A Giese
    Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892 0760, USA
    J Exp Med 186:1535-46. 1997
    Mice with a null mutation of the gene encoding interferon consensus sequence-binding protein (ICSBP) develop a chronic myelogenous leukemia-like syndrome and mount impaired responses to certain viral and bacterial infections...
  14. pmc Consensus sequence-based scheme for epidemiological typing of clinical and environmental isolates of Legionella pneumophila
    Valeria Gaia
    Istituto Cantonale di Microbiologia, Bellinzona, Switherland
    J Clin Microbiol 43:2047-52. 2005
    ..This consensus method will assist in the epidemiological investigation of L. pneumophila infections, especially travel-associated cases, by which it will allow a rapid comparison of isolates obtained in more than one country...
  15. ncbi A novel family of ubiquitous heavy metal ion transport proteins
    I T Paulsen
    Department of Biology, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Membr Biol 156:99-103. 1997
    ..It allows functional predictions for some uncharacterized members of this family. A signature sequence specific for the CDF family is derived...
  16. pmc Role of the Pseudomonas aeruginosa oxyR-recG operon in oxidative stress defense and DNA repair: OxyR-dependent regulation of katB-ankB, ahpB, and ahpC-ahpF
    U A Ochsner
    Department of Microbiology, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA
    J Bacteriol 182:4533-44. 2000
    ..In conclusion, we present evidence that the oxyR-recG locus is essential for oxidative stress defense and for DNA repair...
  17. pmc Regulation of apoptosis in myeloid cells by interferon consensus sequence-binding protein
    L Gabriele
    Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892 0760, USA
    J Exp Med 190:411-21. 1999
    Mice with a null mutation of the gene encoding interferon consensus sequence-binding protein (ICSBP) develop a disease with marked expansion of granulocytes and macrophages that frequently progresses to a fatal blast crisis, thus ..
  18. pmc Initial fitness recovery of HIV-1 is associated with quasispecies heterogeneity and can occur without modifications in the consensus sequence
    Antonio V Borderia
    Virologia Molecular, Centro Nacional de Microbiología CNM, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
    PLoS ONE 5:e10319. 2010
    ..Fitness recovery of HIV-1 "in vitro" was studied using viral clones that had their fitness decreased as a result of plaque-to-plaque passages...
  19. ncbi Binding of PhoP to promoters of phosphate-regulated genes in Streptomyces coelicolor: identification of PHO boxes
    Alberto Sola-Landa
    Instituto de Biotecnología de León INBIOTEC, Parque Cientifico de Leon, Av Real, 1, 24006, Leon, Spain
    Mol Microbiol 56:1373-85. 2005
    ..PHO boxes have been identified by alignment of the six direct repeat units found in those promoter regions. Each direct repeat unit adjusts to the consensus G(G/T)TCAYYYR(G/C)G...
  20. pmc Characterization of prototype foamy virus gag late assembly domain motifs and their role in particle egress and infectivity
    Annett Stange
    Institut fur Virologie, Medizinische Fakultät Carl Gustav Carus, Technische Universitat Dresden, Fetscherstr 74, 01307 Dresden, Germany
    J Virol 79:5466-76. 2005
    ..Taken together these results demonstrate that PFV, like other viruses, requires components of the vacuolar protein sorting (VPS) machinery for egress and enters the VPS pathway through interaction with TSG101...
  21. pmc Human branch point consensus sequence is yUnAy
    Kaiping Gao
    Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466 8550, Japan
    Nucleic Acids Res 36:2257-67. 2008
    ..Our analysis demonstrates that the human BPSs are more degenerative than we have expected and that the human BPSs are likely to be recognized in combination with the polypyrimidine tract and/or the other splicing cis-elements...
  22. ncbi Regulation of Escherichia coli cell envelope proteins involved in protein folding and degradation by the Cpx two-component system
    J Pogliano
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 11:1169-82. 1997
    ..coli genes. These findings suggest a potentially extensive Cpx regulon including genes transcribed by sigma70 and sigma(E), which encode factors involved in protein folding as well as other cellular functions...
  23. pmc Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme
    M Ibba
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 93:6953-8. 1996
    ..The ability of tRNA to optimize amino acid recognition reveals a novel mechanism for maintaining translational fidelity and also provides a strong basis for the coevolution of tRNAs and their cognate synthetases...
  24. ncbi Linear motif atlas for phosphorylation-dependent signaling
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Sci Signal 1:ra2. 2008
    ..NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), ..
  25. pmc PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype
    Petr Danecek
    Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555 0857, USA
    J Mol Biol 396:550-63. 2010
    ..Computational methods are needed to design multivalent vaccines against flaviviruses (FVs) such as the West Nile virus or the dengue virus (DENV)...
  26. ncbi Structure and function of IRF-7
    Luwen Zhang
    Nebraska Center for Virology, UNL Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
    J Interferon Cytokine Res 22:95-101. 2002
    ..Other than its functions in EBV latency, IRF-7 has been identified as one of the major players in virally induced IFN production that is central to innate immunity. Thus, IRF-7 plays important roles in a variety of biologic systems...
  27. ncbi DNA sequence recognition by Pax proteins: bipartite structure of the paired domain and its binding site
    T Czerny
    Research Institute of Molecular Pathology, Vienna, Austria
    Genes Dev 7:2048-61. 1993
    ..of BSAP-binding sites made it possible to unequivocally align all known BSAP-binding sites and to deduce a consensus sequence consisting of two distinct half sites...
  28. pmc Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance
    Han Suk Kim
    Cornell University, Department of Plant Pathology, 360 Plant Science Building, Ithaca, New York 14853, USA
    Plant Cell 14:1469-82. 2002
    ..We propose the existence of a novel defense response that is independent of SAR and negatively regulated in Arabidopsis by SON1 through the ubiquitin-proteosome pathway...
  29. ncbi SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting
    M S Rodriguez
    School of Biology, Biomolecular Sciences Building, University of St. Andrews, St. Andrews, Fife KY169ST, United Kingdom
    J Biol Chem 276:12654-9. 2001
    ..Thus, protein substrates must be targeted to the nucleus to undergo SUMO-1 conjugation...
  30. pmc Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships
    Ken Daigoro Yokoyama
    Biology Department, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Nucleic Acids Res 37:e92. 2009
    ..This offers a novel means by which to predict sequence elements with a collective role in gene regulation...
  31. pmc Identification of the differential distribution patterns of mRNAs and consensus binding sequences for mouse DAF-16 homologues
    T Furuyama
    Laboratory of Genetics of Aging, Department of Molecular Genetic Research, National Institute for Longevity Sciences NILS, 36 3 Gengo, Morioka, Oobu, Aichi 474 8522, Japan
    Biochem J 349:629-34. 2000
    ....
  32. pmc Limb-girdle muscular dystrophy type 2H associated with mutation in TRIM32, a putative E3-ubiquitin-ligase gene
    Patrick Frosk
    Departments of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
    Am J Hum Genet 70:663-72. 2002
    ..Although the function of TRIM32 is unknown, current knowledge of the domain structure of this protein suggests that it may be an E3-ubiquitin ligase. If proven, this represents a new pathogenic mechanism leading to muscular dystrophy...
  33. pmc A base-specific recognition signal in the 5' consensus sequence of rotavirus plus-strand RNAs promotes replication of the double-stranded RNA genome segments
    M Alejandra Tortorici
    Laboratory of Infectious Diseases, NIAID, NIH, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892, USA
    RNA 12:133-46. 2006
    ..The 5' recognition signal is associated with the G2 residue of the 5'-consensus sequence, a residue that shows absolute conservation among all rotavirus groups (A, B, and C) examined to date...
  34. ncbi Isolation of a prokaryotic metallothionein locus and analysis of transcriptional control by trace metal ions
    J W Huckle
    Department of Biological Sciences, University of Durham, UK
    Mol Microbiol 7:177-87. 1993
    ....
  35. pmc Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites
    Søren F Schmidt
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense M, Denmark
    BMC Genomics 12:152. 2011
    ..We and others have previously shown that binding sites of these two transcription factors show a high degree of overlap and are associated with the majority of genes upregulated during differentiation of murine 3T3-L1 adipocytes...
  36. ncbi Identification of novel consensus CD4 T-cell epitopes from clade B HIV-1 whole genome that are frequently recognized by HIV-1 infected patients
    Simone G Fonseca
    Division of Clinical Immunology and Allergy, Department of Medicine, University of Sao Paulo School of Medicine, Brazil
    AIDS 20:2263-73. 2006
    To identify promiscuous and potentially protective human CD4 T-cell epitopes in most conserved regions within the protein-coding genome of HIV-1 clade B consensus sequence.
  37. pmc Divergent and convergent evolution after a common-source outbreak of hepatitis C virus
    Stuart C Ray
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
    J Exp Med 201:1753-9. 2005
    ..These data suggest that vaccines for genetically diverse viruses may be more effective if they represent consensus sequence, rather than a human isolate.
  38. ncbi The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences
    M Krawczak
    Abteilung Humangenetik, Medizinische Hochschule, Hannover, Federal Republic of Germany
    Hum Genet 90:41-54. 1992
    ..Splice sites of intermediate similarity to the consensus sequence may thus be more prone to the deleterious effects of mutation...
  39. pmc Addition of neuA, the gene encoding N-acylneuraminate cytidylyl transferase, increases the discriminatory ability of the consensus sequence-based scheme for typing Legionella pneumophila serogroup 1 strains
    Sandra Ratzow
    Institut fur Medizinische Mikrobiologie und Hygiene, TU Dresden, Fiedlerstrasse 42, D 01307 Dresden, Germany
    J Clin Microbiol 45:1965-8. 2007
    ..932 to 0.963) and subdivided some known large common complexes (e.g., 1,4,3,1,1,1). This modification to the standard method is proposed as the method of choice in the epidemiological investigation of L. pneumophila infections...
  40. pmc Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae
    Birgitte Regenberg
    Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe Universitat, Max von Laue Str, 9, 60438 Frankfurt am Main, Germany
    Genome Biol 7:R107. 2006
    ..We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation times varying between 2 and 35 hours...
  41. ncbi A novel ligand-binding domain involved in regulation of amino acid metabolism in prokaryotes
    Thijs J G Ettema
    Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, NL 6307 CT Wageningen, The Netherlands
    J Biol Chem 277:37464-8. 2002
    ..Both domains appear to play analogous roles in controlling key steps in amino acid metabolism at the level of gene expression as well as enzyme activity...
  42. ncbi Identification and distinct regulation of yeast TATA box-containing genes
    Andrew D Basehoar
    Graduate Program in Statistics, The Pennsylvania State University, University Park, PA 16802, USA
    Cell 116:699-709. 2004
    ..Transcriptional regulation in yeast appears to be mechanistically bipolar, possibly reflecting a need to balance inducible stress-related responses with constitutive housekeeping functions...
  43. ncbi The LINEs and SINEs of Entamoeba histolytica: comparative analysis and genomic distribution
    Abhijeet A Bakre
    School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
    Exp Parasitol 110:207-13. 2005
    ..The elements were very frequently located close to protein-coding genes and other EhLINEs/SINEs. The possible influence of these elements on expression of neighboring genes needs to be determined...
  44. pmc MATLIGN: a motif clustering, comparison and matching tool
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 8:189. 2007
    ..Efficient post-processing, for example, reduces the redundancy of the motifs predicted and enables them to be annotated...
  45. pmc Diversity in nucleotide binding site-leucine-rich repeat genes in cereals
    Jianfa Bai
    Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506 5502, USA
    Genome Res 12:1871-84. 2002
    ..The resistance gene repertoire of grasses has changed from that of dicots in their independent evolution since the two groups diverged. It is not clear whether this reflects a difference in downstream defense signaling pathways...
  46. pmc ESEfinder: A web resource to identify exonic splicing enhancers
    Luca Cartegni
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 31:3568-71. 2003
    ....
  47. ncbi Nuclear localization of EGF receptor and its potential new role as a transcription factor
    S Y Lin
    Department of Molecular and Cellular Oncology, Breast Cancer Basic Research Program, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Nat Cell Biol 3:802-8. 2001
    ..EGFR might therefore function as a transcription factor to activate genes required for highly proliferating activities...
  48. pmc Regulation of alternative polyadenylation by U1 snRNPs and SRp20
    H Lou
    Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
    Mol Cell Biol 18:4977-85. 1998
    ..exon, exon 4, via factors binding to an intronic enhancer element that contains both 3' and 5' splice site consensus sequence elements...
  49. ncbi The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements
    J W Schwabe
    Medical Research Council Laboratory of Molecular Biology, Cambridge, England
    Cell 75:567-78. 1993
    ..Since all nuclear hormone receptors recognize one or the other of these two consensus half site sequences, this recognition mechanism applies generally to the whole receptor family...
  50. ncbi Real-time DNA sequencing from single polymerase molecules
    JOHN EID
    Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA
    Science 323:133-8. 2009
    ..Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates...
  51. ncbi Cloning and characterization of an extracellular Ca(2+)-sensing receptor from bovine parathyroid
    E M Brown
    Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts
    Nature 366:575-80. 1993
    ....
  52. pmc PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Kajino cho 3 7 2, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 189:5534-41. 2007
    ..and DNase I footprinting assays, the PdhR-binding site (PdhR box) was defined, which includes a palindromic consensus sequence, ATTGGTNNNACCAAT. The binding in vitro of PdhR to the PdhR box decreased in the presence of pyruvate...
  53. ncbi Structure and distribution of specific cis-elements for transcriptional regulation of PHO84 in Saccharomyces cerevisiae
    N Ogawa
    Department of Biotechnology, Faculty of Engineering, Osaka University, Japan
    Mol Gen Genet 249:406-16. 1995
    ..The UAS function of the GCACGTTTT motif with respect to the Pi signal depends on its orientation in the promoter sequence...
  54. ncbi Amino acid sequence studies on endocuticular proteins from the desert locust, Schistocerca gregaria
    S O Andersen
    August Krogh Institute, Copenhagen University, Denmark
    Insect Biochem Mol Biol 28:421-34. 1998
    ..All the proteins contain the Rebers-Riddiford consensus sequence commonly found in cuticular proteins...
  55. pmc The N-acylneuraminate cytidyltransferase gene, neuA, is heterogenous in Legionella pneumophila strains but can be used as a marker for epidemiological typing in the consensus sequence-based typing scheme
    Claudia Farhat
    Institut fur Medizinische Mikrobiologie und Hygiene, TU Dresden, Fiedlerstrasse 42, D 01307 Dresden, Germany
    J Clin Microbiol 49:4052-8. 2011
    ..The new primers can be used to amplify and sequence the neuA gene in all strains and can substitute for the standard primers. This offers the possibility of assigning an ST to all strains of L. pneumophila...
  56. pmc DupMasker: a tool for annotating primate segmental duplications
    Zhaoshi Jiang
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Genome Res 18:1362-8. 2008
    ..We predict this tool will be valuable in the annotation of large-insert sequence clones, allowing putative unique and duplicated regions of the genomes to be annotated prior to whole genome assembly comparisons...
  57. pmc Life or death: p53-induced apoptosis requires DNA binding cooperativity
    Katharina Schlereth
    Molecular Oncology, Philipps University Marburg, Marburg, Germany
    Cell Cycle 9:4068-76. 2010
    ..Modulating p53 interactions within the tetramer could therefore present a novel promising strategy to fine-tune p53-based cell fate decisions...
  58. ncbi A consensus sequence for long-chain fatty-acid alcohol oxidases from Candida identifies a family of genes involved in lipid omega-oxidation in yeast with homologues in plants and bacteria
    S Vanhanen
    Lipid Molecular Biology Group, Department of Biological Sciences, University of Durham, South Road, Durham DH1 3LE, United Kingdom
    J Biol Chem 275:4445-52. 2000
    ..The conservation of sequence between yeast, plants, and bacteria suggests that an as yet undescribed family of long-chain fatty-acid oxidases exists in both eukaryotes and prokaryotes...
  59. ncbi DNA uptake signal sequences in naturally transformable bacteria
    H O Smith
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Res Microbiol 150:603-16. 1999
    ..Neisseria meningitidis contains 1891 copies of the USS sequence 5'-GCCGTCTGAA. The USSs are often found in the base paired stem of transcription terminators...
  60. ncbi Evolutionary inventions and continuity of CORE-SINEs in mammals
    N Gilbert
    Centre de Recherche de l Hôpital Sainte Justine, Centre de cancérologie Charles Bruneau, Montreal, H3T 1C5, Canada
    J Mol Biol 298:365-77. 2000
    ..The proposed mechanism suggests that such an adaptation to the changing amplification machinery facilitated the survival and prosperity of CORE-elements over long evolutionary periods in different lineages...
  61. ncbi Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network
    Yu Chih Lo
    Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Neihu 114, Taiwan
    J Mol Biol 330:539-51. 2003
    ..most SGNH-hydrolases have low sequence identities and presently there is no clear criterion to define consensus sequence blocks...
  62. ncbi Identification of functional sine oculis motifs in the autoregulatory element of its own gene, in the eyeless enhancer and in the signalling gene hedgehog
    Tobias Pauli
    Biozentrum, University of Basel, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    Development 132:2771-82. 2005
    ..Using the emerging consensus sequence for SO-DNA binding we performed a genome-wide search and have thereby been able to identify eyeless as well ..
  63. pmc Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP
    Kevin C McGarry
    Department of Biological Sciences, Florida Institute of Technology, 150 West University Boulevard, Melbourne, FL 32901, USA
    Proc Natl Acad Sci U S A 101:2811-6. 2004
    ..necessary and sufficient for initial DNA strand separation, but the five DnaA-binding sites (R boxes) with consensus sequence 5'TGTGNAT/AAA bind both active ATP-DnaA and inactive ADP-DnaA with equal affinity...
  64. ncbi A novel strategy for the identification of toxinlike structures in spider venom
    Sergey Kozlov
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    Proteins 59:131-40. 2005
    ..Also we showed that toxinlike structures exceed two thirds of the overall database sequences...
  65. ncbi Crystal structure of catechol O-methyltransferase
    J Vidgren
    Orion Corporation, Espoo, Finland
    Nature 368:354-8. 1994
    ..The co-enzyme-binding domain is strikingly similar to that of an AdoMet-dependent DNA methylase, indicating that all AdoMet methylases may have a common structure...
  66. pmc Interactions between Nef and AIP1 proliferate multivesicular bodies and facilitate egress of HIV-1
    Luciana J Costa
    Molecular Virology Laboratory, Dep of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
    Retrovirology 3:33. 2006
    ..In this report, we investigated further the ability of Nef to facilitate the replication of HIV-1...
  67. ncbi Predictive identification of exonic splicing enhancers in human genes
    William G Fairbrother
    Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 297:1007-13. 2002
    ..The motifs identified enable prediction of the splicing phenotypes of exonic mutations in human genes...
  68. ncbi Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication
    P Nash
    Programme in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto M5G 1X5, Canada
    Nature 414:514-21. 2001
    ..Multisite phosphorylation may be a more general mechanism to set thresholds in regulated protein-protein interactions...
  69. ncbi Unique features of the structural model of 'hard' cuticle proteins: implications for chitin-protein interactions and cross-linking in cuticle
    Vassiliki A Iconomidou
    Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
    Insect Biochem Mol Biol 35:553-60. 2005
    ....
  70. ncbi Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos
    Anne E Peaston
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Dev Cell 7:597-606. 2004
    ..We propose that differential TE expression triggers sequential reprogramming of the embryonic genome during the oocyte to embryo transition and in preimplantation embryos...
  71. ncbi Eimeria tenella: identification of secretory and surface proteins from expressed sequence tags
    Christian Klotz
    Department of Molecular Parasitology, Humboldt University, Berlin, Germany
    Exp Parasitol 111:14-23. 2005
    ..For five selected candidate proteins we found that these were indeed secreted. Our approach thus represents an efficient method to identify secretory and surface proteins out of EST databases...
  72. ncbi PTS2 co-receptors: diverse proteins with common features
    Wolfgang Schliebs
    Institut fur Physiologische Chemie, Abt Systembiochemie, Ruhr Universitat Bochum, D 44780 Bochum, Germany
    Biochim Biophys Acta 1763:1605-12. 2006
    ..We provide an overview of the proteins that have been identified as PTS2 co-receptors and discuss their proposed functions...
  73. ncbi Functional significance of repressor element 1 silencing transcription factor (REST) target genes in pancreatic beta cells
    D Martin
    Department of Medicine, University Hospital, CHUV, Lausanne, Switzerland
    Diabetologia 51:1429-39. 2008
    ..Herein, we investigated the biological consequences of a repression of REST target genes by expressing REST in beta cells...
  74. pmc Identical consensus sequence and conserved genomic polymorphism of hepatitis E virus during controlled interspecies transmission
    Jerome Bouquet
    UMR 1161 Virology, Anses, Laboratoire de Sante Animale, Maisons Alfort, France
    J Virol 86:6238-45. 2012
    ..pigs experimentally infected with human hepatitis E virus (HEV) of genotype 3f revealed the same full-length consensus sequence as in the human sample...
  75. pmc A comparative analysis of exome capture
    Jennifer S Parla
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Genome Biol 12:R97. 2011
    ..These analyses help clarify the strengths and limitations of those data as well as systematically identify variables that should be considered in the use of those data...
  76. pmc Sequence-specific recognition of methylated DNA by human zinc-finger proteins
    Nobuhiro Sasai
    CNRS UMR7216, Universite Paris Diderot, Paris, France
    Nucleic Acids Res 38:5015-22. 2010
    ..This suggests that many other sequence-specific methyl binding proteins may exist...
  77. pmc Recognition sequence of a highly conserved DNA binding protein RBP-J kappa
    T Tun
    Department of Medical Chemistry, Kyoto University Faculty of Medicine, Japan
    Nucleic Acids Res 22:965-71. 1994
    ..All these data indicate that the RBP-J kappa protein recognizes a unique core sequence of CGTGGGAA and does not bind to the V(D)J recombination signal without the flanking sequence...
  78. pmc Mutational analysis of the U12-dependent branch site consensus sequence
    Jay E Brock
    Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
    RNA 14:2430-9. 2008
    ..This study investigates the in vivo splicing phenotypes of mutations in the branch site consensus sequence of the U12-dependent intron F from a human NOL1 (P120) minigene...
  79. ncbi Analysis and prediction of leucine-rich nuclear export signals
    Tanja la Cour
    Center for Biological Sequence Analysis, BioCentrum DTU, Technical University of Denmark, Building 208, DK 2800 Lyngby, Denmark
    Protein Eng Des Sel 17:527-36. 2004
    ..We employ both neural networks and hidden Markov models in the prediction algorithm and verify the method on the most recently discovered NESs. The NES predictor (NetNES) is made available for general use at http://www.cbs.dtu.dk/...
  80. ncbi Nuclear export signal consensus sequences defined using a localization-based yeast selection system
    Shunichi Kosugi
    Institute for Advanced Biosciences, Keio University, Tsuruoka 997 0017, Japan
    Traffic 9:2053-62. 2008
    ..However, the NES consensus sequence remains poorly defined, and there are currently no high-throughput methods for identifying NESs...
  81. ncbi The antigen receptor (NCCRP-1) on catfish and zebrafish nonspecific cytotoxic cells belongs to a new gene family characterized by an F-box-associated domain
    Liliana Jaso-Friedmann
    Department of Medical Microbiology and Parasitology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602 7386, USA
    J Mol Evol 54:386-95. 2002
    ..This new gene family includes several F-box domain-containing proteins and a predicted C. elegans protein...
  82. pmc Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family
    Peter C Hollenhorst
    Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
    Genes Dev 21:1882-94. 2007
    ..The specific and redundant DNA-binding modes suggest two distinct roles for members of the ETS transcription factor family...
  83. ncbi TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1
    Dietmar E Martin
    Division of Biochemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    Cell 119:969-79. 2004
    ..Thus, we describe a signaling mechanism linking an environmental sensor to ribosome biogenesis...
  84. pmc Mutations in the mariner transposase: the D,D(35)E consensus sequence is nonfunctional
    A R Lohe
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 94:1293-7. 1997
    ..transposase function is obliterated when the D,D(34)D acidic, ion-binding domain is replaced with the consensus sequence D,D(34)E found in the nematode Tc1 transposase and in many other transposases in the superfamily...
  85. pmc Brachyury proteins regulate target genes through modular binding sites in a cooperative fashion
    Thomas Kusch
    Institut fur Genetik, Universitat zu Koln, 50931 Koln, Germany
    Genes Dev 16:518-29. 2002
    ..We propose that the mechanisms to achieve target gene expression through variable binding sites and through defined protein-protein interactions might be conserved for Brachyury relatives...
  86. pmc Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis
    Sophia L Stone
    Section of Molecular and Cellular Biology, Division of Biological Sciences, University of California, Davis, California 95616, USA
    Plant Physiol 137:13-30. 2005
    ....
  87. ncbi Targets of the cyclin-dependent kinase Cdk1
    Jeffrey A Ubersax
    Department of Physiology, University of California, San Francisco, California 94143, USA
    Nature 425:859-64. 2003
    ..Detailed analysis of these substrates is likely to yield important insights into cell-cycle regulation...
  88. ncbi Potential for retroposition by old Alu subfamilies
    Karla Johanning
    Tulane Cancer Center SL 66, Department of Environmental Health Sciences, Tulane University Medical Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA
    J Mol Evol 56:658-64. 2003
    ..Sequence identity to the left half or the right half of the Alu Sx consensus sequence was evaluated for 4424 complete elements obtained from the human genome draft sequence...
  89. pmc Murine coronavirus with an extended host range uses heparan sulfate as an entry receptor
    Cornelis A M de Haan
    Virology Division, Department of Infectious Diseases and Immunology, Yalelaan 1, 3584CL Utrecht, The Netherlands
    J Virol 79:14451-6. 2005
    ....
  90. ncbi Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking
    S Chen
    Department of Chemistry and The Waksman Institute, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    J Mol Biol 314:63-74. 2001
    ..We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence...
  91. pmc A single base difference between Pit-1 binding sites at the hGH promoter and locus control region specifies distinct Pit-1 conformations and functions
    Brian M Shewchuk
    University of Pennsylvania School of Medicine, 415 Curie Blvd, Philadelphia, PA 19103, USA
    Mol Cell Biol 26:6535-46. 2006
    ..These data support a model in which the Pit-1 binding sites in the hGH LCR allosterically program the bound Pit-1 complex for chromatin activating functions...
  92. pmc The cytoplasmic zinc finger protein ZPR1 accumulates in the nucleolus of proliferating cells
    Z Galcheva-Gargova
    Program in Molecular Medicine, Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Mol Biol Cell 9:2963-71. 1998
    ..These data establish ZPR1 as an essential protein that is required for normal nucleolar function in proliferating cells...
  93. ncbi Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression
    Riccardo Manganelli
    TB Center, The Public Health Research Institute at the International Center for Public Health, Newark, NJ 07103 3506, USA
    Mol Microbiol 45:365-74. 2002
    ..Other genes under sigma(H) control encode transcriptional regulators such as sigB, sigE, and sigH itself...
  94. ncbi Secondary structure prediction for aligned RNA sequences
    Ivo L Hofacker
    Institut fur Theoretische Chemie, Universitat Wien, Wahringerstrasse 17, Austria
    J Mol Biol 319:1059-66. 2002
    ..As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation...
  95. ncbi Tumor suppressor p53 is a direct transcriptional activator of the human bax gene
    T Miyashita
    La Jolla Cancer Research Foundation, California 92037
    Cell 80:293-9. 1995
    ..Taken together, the results suggest that bax is a p53 primary-response gene, presumably involved in a p53-regulated pathway for induction of apoptosis...
  96. ncbi Modified phage peptide libraries as a tool to study specificity of phosphorylation and recognition of tyrosine containing peptides
    L Dente
    Dipartimento di Biologia Università di Roma Tor Vergata, Rome, Italy
    J Mol Biol 269:694-703. 1997
    ..conforming to this sequence is a better substrate than a second peptide designed to be in accord with the consensus sequence recognised by the Fyn SH2 domain...
  97. ncbi Restless 5S: the re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants
    Susann Wicke
    Institute for Evolution and Biodiversity, University of Muenster, Huefferstr 1, D 48149 Muenster, Germany
    Mol Phylogenet Evol 61:321-32. 2011
    ..Several putative scenarios and mechanisms involved in the concerted relocation of hundreds of 5S rRNA gene copies are discussed...
  98. pmc Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators
    Maria A Schumacher
    Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Nucleic Acids Res 39:2931-42. 2011
    ..Indeed, biochemical data show that CcpA-(HPr-Ser46-P) binds the three cre sites with similar affinities. Thus, the data reveal properties that license this protein to function as a global transcription regulator...
  99. pmc Functional noncoding sequences derived from SINEs in the mammalian genome
    Hidenori Nishihara
    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
    Genome Res 16:864-74. 2006
    ..The conservation is strongest over the central domain. Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality...
  100. pmc RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing
    C G Burd
    Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia 19104 6148
    EMBO J 13:1197-204. 1994
    ..We also show that this oligoribonucleotide, as well as two others containing 5' and 3' pre-mRNA splice sites, are potent inhibitors of in vitro pre-mRNA splicing...
  101. pmc Protein-DNA binding specificity predictions with structural models
    Alexandre V Morozov
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 33:5781-98. 2005
    ..The predictive capability of the model is tested against another model based only on the knowledge of the consensus sequence and the number of contacts between amino acids and DNA bases...

Research Grants63

  1. ICSBP Function During Myeloid Differentiation
    ELIZABETH ANN EKLUND; Fiscal Year: 2011
    DESCRIPTION (provided by applicant): Several lines of evidence suggest that the interferon consensus sequence binding protein (ICSBP or IRF8) functions as a myeloid leukemia tumor-suppressor...
  2. Novel Bioconjugate Vaccines to Prevent Staphylococcus aureus Infection
    JEAN CLAIRE LEE; Fiscal Year: 2013
    ..A novel Campylobacter enzyme called PglB is able to transfer an oligosaccharide to a protein consensus sequence, thereby allowing the production of glycoproteins in bacterial cells...
  3. Molecular Mechanisms of Disease Progression in Myeloid Malignancy
    ELIZABETH ANN EKLUND; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): The Interferon Consensus Sequence Binding Protein (Icsbp) is an interferon regulatory transcription factor that functions as a tumor-suppressor (also referred to as Irf8)...
  4. DlaT as a transcriptional regulator in non-replicating Mycobacterium tuberculosis
    Ruslana Bryk; Fiscal Year: 2012
    ..Information from ChIP-Seq will be used to deduce the putative DlaT DNA-binding consensus sequence. Current application aims at elucidating the mechanism behind DlaT's function as a transcriptional ..
  5. Structural Studies of RNA Maturation and Processing
    Christopher D Lima; Fiscal Year: 2013
    ..II) after it is phosphorylated on serine residues within its C-terminal tandem heptapeptide repeats with the consensus sequence Y1S2P3T4S5P6S7...
  6. Mechanisms of viral proteases in coronavirus replication and pathogenesis
    Andrew D Mesecar; Fiscal Year: 2013
    ..the replicase polyprotein at three sites using a consensus recognition site of LXGG, similar to the consensus sequence recognized by de-ubiquitinating enzymes (DUBs)...
  7. The role of ICSBP in the pathogenesis of chronic myeloid leukemia
    ELIZABETH ANN EKLUND; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): The Interferon Consensus Sequence Binding Protein (Icsbp or Irf8) is a transcription factor that functions as a leukemia-suppressor...
  8. Elucidating the A. baumannii response to calprotectin-mediated zinc starvation
    BRITTANY MORTENSEN; Fiscal Year: 2013
    ..A search for this consensus sequence within the A. baumannii genome identified additional genes that may be regulated by Zur and Zn...
  9. Research and Development of a Novel System to Produce Polysaccharide Conjugate Va
    Peng George Wang; Fiscal Year: 2013
    ..to transfer a variety of PS (from different bacteria) from its diphospho-undecaprenyl forms to the Asn of a consensus sequence of the target protein in the periplasm...
  10. The mechanism of mRNA recruitment to the human ribosome.
    Christopher S Fraser; Fiscal Year: 2013
    ..Characterize the association of eIF4G with eIF3 and the 40S subunit. We will determine the consensus sequence in eIF4G that binds to eIF3...
  11. In vivo phenotypic effects of naturally occuring sequence variations in WNV
    Robin M Moudy; Fiscal Year: 2010
    ..We will also determine whether the consensus sequence differences between the two genotypes of WNV are sufficient to cause the observed phenotypic differences by ..
  12. Pre-osteoclast fusion
    Paul R Odgren; Fiscal Year: 2013
    ..OC precursors by RANKL;2) predicted topology of transmembrane (TM) helices;3) presence of a DC-STAMP family consensus sequence in the C-terminal half of OC-STAMP;4) suppression of formation of multinucleated osteoclasts in vivo and in ..
  13. The Viral Life Cycle of Human Endogenous Retrovirus Type K
    Derek Dube; Fiscal Year: 2013
    ..to be identified, two groups have recently resuscitated infectious HERV-K progenitor viruses based on the consensus sequence of the most complete family members...
  14. Structural and Functional Studies of the Novel DBD Domain of MKP5
    Amjad Farooq; Fiscal Year: 2012
    ..MKP5 contains a novel DNA-binding and dimerization (DBD) domain that specifically interacts with DNA at the consensus sequence TGACTCA recognized by the transcription factor AP1 and found within promoters of genes whose products are ..
  15. The regulatory function of DNA methylation in Mycobacterium tuberculosis
    SCARLET SARA SHELL; Fiscal Year: 2012
    ..Study design: The methylation consensus sequence determined in preliminary studies will be used to map Mrh sites across the genome and predict loci that may ..
  16. The Role of SaeR/S During Staphylococcus aureus Skin Infections
    Jovanka M Voyich; Fiscal Year: 2012
    ..extracellular virulence genes down-regulated in USA300?saeR/S and direct binding of recombinant SaeR to a consensus sequence within virulence gene promoters...
  17. REGULATION OF TRYPANOSOME DNA REPLICATION
    DAN RAY; Fiscal Year: 2009
    ..In earlier work with C. fasciculata we identified an octamer consensus sequence required for S-phase expression of several genes and also two protein complexes that bind to the octamer ..
  18. NMR STUDIES OF BACTERIAL REGULATORY PROTEINS
    John Cavanagh; Fiscal Year: 2012
    ..The mechanism by which they target their DNA targets is novel and very different than the classical "consensus sequence recognition" model...
  19. Role of the Staphylococcus aureus SaeR/S Regulatory System in Neutrophil Evasion
    Jovanka M Voyich; Fiscal Year: 2013
    ..extracellular virulence genes down- regulated in saeR/S and direct binding of recombinant SaeR to a consensus sequence within several of these virulence gene promoters...
  20. Mechanisms of retinal angiogenesis
    Gadiparthi N Rao; Fiscal Year: 2013
    ..to a basic/leucine zipper (bZIP) family of transcriptional factors and possess the ability to bind o the consensus sequence TGAC/GTCA in the promoter regions of genes enhancing their expression in response to a wide variety of ..
  21. MECHANISM OF PRE-MRNA SPLICING
    MAGDA KONARSKA; Fiscal Year: 2012
    ..The proposed studies, aimed at understanding the function of the yeast spliceosome, are expected to explain some fundamental properties of alternative splicing in human cells. ..
  22. BCG as an HIV vaccine vector
    Anna Lise Williamson; Fiscal Year: 2011
    ..Genes were selected from recently transmitted HIV and closest to the South African consensus sequence. As it is likely that a vaccine will be more effective with more genes, this project will initially focus on ..
  23. The Role of 5-HT6 Receptors in Primary Neuronal Cilia
    John F Neumaier; Fiscal Year: 2013
    ..Ciliary localization is thought to be governed by a discrete consensus sequence in the third intracellular loop of GPCRs including 5-HT6 and a small set of other proteins...
  24. Live Brain Gene Detection in Drug Exposure Subjects after Acupuncture Treatment
    Jiaqian Ren; Fiscal Year: 2011
    ..This method uses DNA with antisense sequence to the target mRNA or DNA with consensus sequence for AP-1 binding...
  25. Repeat-Proteins;Stability, Folding Kinetics &Evolution
    DOUGLAS E BARRICK; Fiscal Year: 2012
    ..b>Consensus sequence variants will be used to resolve which types of interactions give rise to the extraordinary cooperativity we ..
  26. Novel H1N1 influenza protection via cross-reactive immunity
    ANNE SEARLS DEGROOT; Fiscal Year: 2012
    ..The aims for this project are to: (1) Synthesize and validate "immunogenic consensus sequence" cross-conserved influenza class II epitopes, using available influenza sequences as our point of departure, ..
  27. NMR studies of collagen model peptides and their interactions with collagen recep
    JEAN S BAUM; Fiscal Year: 2013
    ..2) Using statistical approaches, develop consensus sequence patterns that define lethal and nonlethal phenotypes in OI;these will be used to begin to establish ..
  28. Epigenetic regulation of neuropathic pain: Role of native KV1.2 antisense RNA
    Yuan Xiang Tao; Fiscal Year: 2013
    ..Furthermore, we will examine whether Kv1.2 AS RNA is up- regulated as a result of MZF-1 binding to the consensus sequence on the Kv1.2 AS gene promoter in the injured DRG after peripheral nerve injury...
  29. Molecular Means for 3'Splice Site Recognition by U2AF35
    Kholiswa M Laird; Fiscal Year: 2013
    ..an essential auxiliary protein factor, U2AF, binds to a polypyrimidine and 'AG'dinucleotide consensus sequence at the 3'splice site...
  30. CRE Mediated Transcription in Epileptogenesis
    Brenda E Porter; Fiscal Year: 2012
    ..The CREB family of transcription factors CREB, CREM and ICER bind to a consensus sequence of DNA called CRE (cyclic-amp response element) sites, and then activate or inhibit transcription of a large ..
  31. High Throughput Modular Microfluidic Systems for Drug Discovery/Development
    Steven Allan Soper; Fiscal Year: 2010
    ..L1-EN induces double-strand breaks via a TTTT'AA consensus sequence and can contribute to genetic damage responsible for cellular aging, cancer formation or progression...
  32. Maintenance and Development of RepeatMasker and RepeatModeler
    ARIAN FREDERICUS ANTHONIUS SMIT; Fiscal Year: 2012
    ..c) The maintenance of the DNA consensus sequence database with many RepeatMasker-specific metadata, the Transposable Element protein database, and the ..
  33. Protective cellular immune responses in HIV-1 discordant couples
    Carey Farquhar; Fiscal Year: 2010
    ..At enrollment, CD8+ and CD4+ T cell responses against peptides derived from a consensus sequence clade A HIV-1 will be measured in the uninfected partner using ELISpot assays and intracellular cytokine ..
  34. CONTROL OF CELL FUNCTION VIA SELECTIVE MRNA TRANSLATION
    Lee Gehrke; Fiscal Year: 2002
    ..Three significant accomplishments of the current funding period are 1) the discovery of a novel RNA binding consensus sequence in the viral coat proteins, 2) the identification, through use of chemical modification interference and ..
  35. GP91-PHOX TRANSCRIPTION FACTORS AND HEMATOPOIESIS
    Elizabeth Eklund; Fiscal Year: 2000
    ..The gp91phox promoter contains no g-activation site consensus sequence and IFN-g stimulated gp91phox transcription requires new protein synthesis...
  36. STRUCTURE OF VIRAL RNA IN RIBOSOMAL FRAMESHIFTING
    Alexander Rich; Fiscal Year: 2004
    ..The slippery shift site on the messenger RNA has an X XXY YYN consensus sequence (the initial reading frame is indicated, and bases X and Y can be identical)...
  37. LH ACTION IN OVARIAN CELL DIFFERENTIATION
    Joanne Richards; Fiscal Year: 2007
    ..Using deletional and mutational analyses, we have determined that the rat PGS-2 promoter contains an E-box consensus sequence that is essential for transcription of PGS-2 promoter-reporter transgenes in granulosa cells and binds ..
  38. Molecular basis of congenital disorders of glycosylation: mechanisms of oligosach
    Smita Mohanty; Fiscal Year: 2010
    ..The C-terminal domain of the Stt3p subunit is shown to recognize the glycosylation site present in the consensus sequence on nascent protein...
  39. GENETIC REGULATORY MECHANISMS IN NEUROSPORA
    Mary Case; Fiscal Year: 1990
    ..Present data suggest that this target may be a 16 bp consensus sequence with dyad symmetry (i.e., an upstream activator sequence - UASQ) located 5' to each qa gene...
  40. CALCIUM INDEPENDENT PLA2 AND ISCHEMIC CELL INJURY
    Didier Portilla; Fiscal Year: 2000
    ..Furthermore, it also contains the sequence U-F-S-Q-G, which agrees with the consensus sequence surrounding active site serines, G-X-S-X-U, observed in many carboxyl esterases including lipases...
  41. CONTROL OF IMMUNOGLOBULIN SYNTHESIS
    Ursula Storb; Fiscal Year: 2001
    ..Rearrangement signal sequences flanking the V,D and J gene joining partners must have the correct consensus sequence. Thus, one has some general picture of the rearrangement process, but many of the details of the molecular ..
  42. REGULATION OF POLYCYCLIC AROMATIC HYDROCARBON TOXICITY
    WILLIAM HOUSER; Fiscal Year: 1992
    ..gene fusion assays with the reporter gene chloramphenicol acetyltransferase; 2) Determine the location and consensus sequence of the PAH-responsive proximal cis-element in the 5'-flanking region of the rat P45OIAl gene using ..
  43. NOVEL FAS BINDING PROTEIN AND ITS ROLE IN DISEASE
    Raif Geha; Fiscal Year: 1999
    ..Wild type FAP, but not a mutant in which Cys93 in the consensus sequence of the active site for ubiquitin conjugation was replaced by Ser, complemented UBC9 temperature sensitive ..
  44. NOVEL GENE ASSOCIATED WITH CHONDROCYTE DIFFERENTIATION
    Paul Reynolds; Fiscal Year: 2001
    ..is a C-terminal extension of the 318 amino acid gene product, is at least 10 fold more abundant, and has a consensus sequence at the C-terminal that targets proteins to the lumen of the endoplasmic reticulum...
  45. MOLECULAR MECHANISM OF ACTION OF SOMATOSTATIN
    Andrea Todisco; Fiscal Year: 1999
    ..to form a heterodimeric transcription factor complex (AP-1) that binds specifically to DNA elements of the consensus sequence TGACTCA and stimulates the transcription of nearby promoters...
  46. The role of phospholipase C in Trypanosoma cruzi
    Silvia Moreno; Fiscal Year: 2001
    ..far, the deduced amino acid sequence of TcPI-PLC revealed some unique features such as an N-myristoylation consensus sequence at its N-terminal end, lack o an apparent PH domain and a highly charged linker region between the catalytic ..
  47. HIV-1 diversity in Optimized Vaccine Seletion
    Karina Yusim; Fiscal Year: 2005
    ..We would start from a consensus sequence, and incorporate the most common amino acid in highly conserved positions...
  48. INFERRING CHROMOSOME ARCHITECTURE FROM GENOMIC SEQUENCE
    Craig Benham; Fiscal Year: 2002
    ..underlying scaffold attachment and its regulatory effects has been hampered by the fact that S/MARs have no consensus sequence associated with them...
  49. BIOSYNTHESIS OF BLOOD CLOTTING PROTEINS
    Bruce Furie; Fiscal Year: 2001
    ..the gamma carboxylation recognition site which directs gamma carboxylation, and a propeptide cleavage consensus sequence. The current proposal aims to define the consensus sequence for the gamma carboxylation recognition site ..
  50. Regulation of Receptor Tyrosine Kinases
    Daniel Donoghue; Fiscal Year: 2005
    ..In Aim 1, using consensus sequence transmembrane domains to provide constitutive dimerization, we will examine rotational coupling for FGFR3, ..
  51. Cis and Trans acting factors for HHV8 lytic replication
    Gregory Pari; Fiscal Year: 2009
    ..three AP1 transcription factor binding sites, an ORF50 response element (RE) and a downstream TATA consensus sequence are all required for efficient amplification of oriLyt...
  52. Biology-Pathology of Arbovirus Persistence in a Mosquito Host
    Doria Bowers; Fiscal Year: 2007
    ..SVHR and the cDNA clone, pTR339 a molecular construct retaining the consensus sequence of AR339, will be used to produce wild type virus. Infectious blood meals will be proffered to Ae...
  53. Gene Amplification-Sciarid DNA Puffs
    SUSAN GERBI; Fiscal Year: 2006
    ..identify sequences in the 160 bp fragment required for ORC binding, including a functional test of a 14 bp consensus sequence found both at the left and right replication start sites in the Sciara 11/9A origin...
  54. Shutdown of Translation and Ischemia/Stroke-Induced Cell Death
    Wulf Paschen; Fiscal Year: 2009
    ..the respective mRNA under conditions associated with suppression of protein synthesis, and a promoter with a consensus sequence for the binding of transcription factors known to be activated after ischemia...
  55. PROTEIN TYROSINE PHOSPHATASES AT NEUROMUSCULAR JUNCTION
    Lin Mei; Fiscal Year: 1999
    ..different protein tyrosine phosphatases have been identified from the rat skeletal muscle based on the consensus sequence of previously characterized tyrosine phosphatases, including PTP1D, a cytoplasmic phosphatase containing two ..
  56. IMPACT OF 5FU ON THE STRUCTURE OF THE U4/U6 COMPLEX
    WILLIAM GMEINER; Fiscal Year: 2000
    ..Each of the spliceosomal snRNAs (except U6 snRNA) contains an Sm binding site (consensus sequence in S. cerevisae = AAUUUUUGG)...
  57. Novel mode of p53 mediated repression the mdri paradigm
    KATHLEEN SCOTTO; Fiscal Year: 2004
    p53 activates transcription by binding as a tetramer to a consensus sequence (the p53 HH site) within the promoter of target genes...
  58. Transmembrane Domains of Receptor Tyrosine Kinases
    Daniel Donoghue; Fiscal Year: 2001
    ..Using consensus sequence transmembrane domains to provide constitutive dimerization, we will examine rotational coupling of the ..
  59. EPIDERMAL TRANS-ACTING FACTORS IN SKIN DEVELOPMENT
    Renata Polakowska; Fiscal Year: 1993
    ..trans-acting factor(s) including their role in development we will take advantage of the existence of consensus sequence homology between the 50K, 56K, 67K keratin and involucrin epidermal genes and a keratinocyte-dependent (KD) ..
  60. HORMONAL REGULATION OF INSULIN RECEPTORS
    Ira Goldfine; Fiscal Year: 1993
    ..the promoter region of the IR gene, and have identified a potential glucocorticoid response element (GRE) consensus sequence in the first intron...
  61. INTEGRATED DNA SEQUENCING SYSTEM
    Stevan Jovanovich; Fiscal Year: 2001
    DESCRIPTION: (Applicant's Abstract) The Human Genome Project is rapidly developing a draft consensus sequence of the Human Genome...
  62. MOLECULAR BASIS OF ALPHAVIRUS NEUROVIRULENCE
    William Klimstra; Fiscal Year: 2004
    ..In the previous grant period we deduced a consensus sequence for the prototype alphavirus, Sindbis (SB), eliminating mutations for cell culture-adaptation and ..
  63. Nutritional Regulation of Catalase and Colorectal Cancer
    Sumio Yano; Fiscal Year: 2002
    ..catalase binds Grb2 and Pl3Kp85, regulatory proteins of insulin signaling, and that catalase contains a consensus sequence of "suppressor of cytokine signaling" that enables it to bind elongin c, an essential factor for elongation ..