Consensus sequence. Medical search

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.

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

General agreement or collective opinion; the judgment arrived at by most of those concerned.

The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.

DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.

The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.

A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).

The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.

Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.

Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

Presentations of summary statements representing the majority agreement of physicians, scientists, and other professionals convening for the purpose of reaching a consensus--often with findings and recommendations--on a subject of interest. The Conference, consisting of participants representing the scientific and lay viewpoints, is a significant means of evaluating current medical thought and reflects the latest advances in research for the respective field being addressed.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.

A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.

The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.

Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.

Nucleic acid sequences involved in regulating the expression of genes.

Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.

Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.

Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.

Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).

RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.

A family of transcription factors that share an N-terminal HELIX-TURN-HELIX MOTIF and bind INTERFERON-inducible promoters to control GENE expression. IRF proteins bind specific DNA sequences such as interferon-stimulated response elements, interferon regulatory elements, and the interferon consensus sequence.

Established cell cultures that have the potential to propagate indefinitely.

Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.

The functional hereditary units of BACTERIA.

Proteins found in any species of bacterium.

A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.

Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.

In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.

Deoxyribonucleic acid that makes up the genetic material of bacteria.

Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.

Proteins prepared by recombinant DNA technology.

Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.

A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.

The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.

The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.

A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.

The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.

The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.

In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.

Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.

An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.

The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.

Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.

A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.

The relationships of groups of organisms as reflected by their genetic makeup.

A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.

Deoxyribonucleic acid that makes up the genetic material of fungi.

Deletion of sequences of nucleic acids from the genetic material of an individual.

A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.

Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.

Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.

An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.

An iterative questionnaire designed to measure consensus among individual responses. In the classic Delphi approach, there is no interaction between responder and interviewer.

A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.

Any method used for determining the location of and relative distances between genes on a chromosome.

The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.

Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.

Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.

Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.

A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.

Biochemical identification of mutational changes in a nucleotide sequence.

An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.

The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.

A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).

Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.

Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.

Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.

Transport proteins that carry specific substances in the blood or across cell membranes.

The chemical or biochemical addition of carbohydrate or glycosyl groups to other chemicals, especially peptides or proteins. Glycosyl transferases are used in this biochemical reaction.

Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.

Two-dimensional separation and analysis of nucleotides.

The rate dynamics in chemical or physical systems.

Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.

Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.

The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.

A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).

Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.

A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.

Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.

A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.

A proprotein convertase with specificity for the proproteins of PROALBUMIN; COMPLEMENT 3C; and VON WILLEBRAND FACTOR. It has specificity for cleavage near paired ARGININE residues that are separated by two amino acids.

Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.

Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.

A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).

Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)

The functional hereditary units of FUNGI.

Deoxyribonucleic acid that makes up the genetic material of viruses.

A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)

RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.

The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.

The complete genetic complement contained in a DNA or RNA molecule in a virus.

Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)

The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.

The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.

A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.

Genotypic differences observed among individuals in a population.

Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.

The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.

Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.

Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.

An interferon regulatory factor that represses transcription of TYPE I INTERFERONS and activates transcription of HISTONE H4.

A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.

Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)

The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.

Ribonucleic acid that makes up the genetic material of viruses.

The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.

Sequential operating programs and data which instruct the functioning of a digital computer.

Proteins found in any species of virus.

Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.

A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.

Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.

Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.

A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.

Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).

Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.

Articles on conferences sponsored by NIH presenting summary statements representing the majority agreement of physicians, scientists, and other professionals convening for the purpose of reaching a consensus on a subject of interest. This heading is used for NIH consensus conferences as a means of scientific communication. In indexing it is viewed as a type of review article and as a tag for any article appearing in any publication of the NIH Office of Medical Applications of Research (OMAR).

Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.

The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.

A protein which is a subunit of RNA polymerase. It effects initiation of specific RNA chains from DNA.

Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.

Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.

A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.

The functional hereditary units of VIRUSES.

Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.

The sum of the weight of all the atoms in a molecule.

Proteins found in any species of fungus.

A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.

Complexes of RNA-binding proteins with ribonucleic acids (RNA).

Actual loss of portion of a chromosome.

The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.

Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.

Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.

A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).

A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids.

Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.

The process by which a DNA molecule is duplicated.

Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.

In eukaryotes, a genetic unit consisting of a noncontiguous group of genes under the control of a single regulator gene. In bacteria, regulons are global regulatory systems involved in the interplay of pleiotropic regulatory domains and consist of several OPERONS.

The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.

Proteins obtained from ESCHERICHIA COLI.

An interferon regulatory factor that binds upstream TRANSCRIPTIONAL REGULATORY ELEMENTS in the GENES for INTERFERON-ALPHA and INTERFERON-BETA. It functions as a transcriptional activator for the INTERFERON TYPE I genes.

A family of Primates of the suborder Strepsirhini containing six genera. The family is distributed in parts of Africa, India, Asia, and the Philippines. The six genera are: Arctocebus (golden potto), GALAGO (bush babies), Loris (slender loris), Nycticebus (slow loris), and Perodicticus (potto). Lorises and pottos are relatively common except for Arctocebus, the golden potto. All are arboreal and nocturnal.

Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.

The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.

A family of SERINE ENDOPEPTIDASES isolated from Bacillus subtilis. EC 3.4.21.-

Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.

Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.

Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.

A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.

Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.

A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.

The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.

Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.

Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.

Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.

Proteins which are synthesized in eukaryotic organisms and bacteria in response to hyperthermia and other environmental stresses. They increase thermal tolerance and perform functions essential to cell survival under these conditions.

Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.

A species of gram-positive bacteria that is a common soil and water saprophyte.

A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.

Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.

Bacterial proteins that are used by BACTERIOPHAGES to incorporate their DNA into the DNA of the "host" bacteria. They are DNA-binding proteins that function in genetic recombination as well as in transcriptional and translational regulation.

DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.

Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.

The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.

The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.

Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).

CELL LINE derived from the ovary of the Chinese hamster, Cricetulus griseus (CRICETULUS). The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells.

Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.

A family of enzymes that catalyze the conversion of ATP and a protein to ADP and a phosphoprotein.

The regulatory elements of an OPERON to which activators or repressors bind thereby effecting the transcription of GENES in the operon.

Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.

A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.

A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.

Serologic tests in which a positive reaction manifested by visible CHEMICAL PRECIPITATION occurs when a soluble ANTIGEN reacts with its precipitins, i.e., ANTIBODIES that can form a precipitate.

A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.

Societies whose membership is limited to physicians.

A species of fruit fly much used in genetics because of the large size of its chromosomes.

Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.

A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.

The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.

A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.

Viruses whose hosts are bacterial cells.

The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.

CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)

The process by which two molecules of the same chemical composition form a condensation product or polymer.

Concomitant activation of pathways downstream of Grb2 and PI 3-kinase is required for MET-mediated metastasis. (1/4818)

The Met tyrosine kinase - the HGF receptor - induces cell transformation and metastasis when constitutively activated. Met signaling is mediated by phosphorylation of two carboxy-terminal tyrosines which act as docking sites for a number of SH2-containing molecules. These include Grb2 and p85 which couple the receptor, respectively, with Ras and PI 3-kinase. We previously showed that a Met mutant designed to obtain preferential coupling with Grb2 (Met2xGrb2) is permissive for motility, increases transformation, but - surprisingly - is impaired in causing invasion and metastasis. In this work we used Met mutants optimized for binding either p85 alone (Met2xPI3K) or p85 and Grb2 (MetPI3K/Grb2) to evaluate the relative importance of Ras and PI 3-kinase as downstream effectors of Met. Met2xPI3K was competent in eliciting motility, but not transformation, invasion, or metastasis. Conversely, MetP13K/Grb2 induced motility, transformation, invasion and metastasis as efficiently as wild type Met. Furthermore, the expression of constitutively active PI 3-kinase in cells transformed by the Met2xGrb2 mutant, fully rescued their ability to invade and metastasize. These data point to a central role for PI 3-kinase in Met-mediated invasiveness, and indicate that simultaneous activation of Ras and PI 3-kinase is required to unleash the Met metastatic potential. (+info)

ATF-2-binding regulatory element is responsible for the Ly49A expression in murine T lymphoid line, EL-4. (2/4818)

To understand the mechanism of Ly49A-expression and its significance in T-cell differentiation, we analyzed the 5'-flanking region of the Ly49A gene in a search for the Ly49A-regulatory element. Since very few known regulatory elements have been found in this region, presumably a novel regulatory sequence(s) could exist. Accordingly, we defined the 13-bp regulatory element, 5'-ATGACGAGGAGGA-3', restricted to Ly49A-expression in EL-4 cells in comparison with two other representative cell lines tested. This element, designated as EL13, proved to be previously undiscovered by homology search and is highly homologous with several virus DNAs. Using EL13 as a probe we have cloned a cDNA encoding a binding protein to EL13. Its deduced nucleotide sequence revealed that EL13-binding protein is almost identical with rat ATF-2. Although ATF-2 is known to bind to cyclic AMP responsive element (CRE), EL13 shares five out of eight nucleotides with this consensus sequence. Our results suggested that ATF-2 may play an important role via binding to EL13 for the expression of Ly49A. These data will provide useful information for understanding T-cell and NK-cell differentiation in murine immune system. (+info)

Identification of a cAMP response element within the glucose- 6-phosphatase hydrolytic subunit gene promoter which is involved in the transcriptional regulation by cAMP and glucocorticoids in H4IIE hepatoma cells. (3/4818)

The expression of a luciferase reporter gene under the control of the human glucose 6-phosphatase gene promoter was stimulated by both dexamethasone and dibutyryl cAMP in H4IIE hepatoma cells. A cis-active element located between nucleotides -161 and -152 in the glucose 6-phosphatase gene promoter was identified and found to be necessary for both basal reporter-gene expression and induction of expression by both dibutyryl cAMP and dexamethasone. Nucleotides -161 to -152 were functionally replaced by the consensus sequence for a cAMP response element. An antibody against the cAMP response element-binding protein caused a supershift in gel-electrophoretic-mobility-shift assays using an oligonucleotide probe representing the glucose 6-phosphatase gene promoter from nucleotides -161 to -152. These results strongly indicate that in H4IIE cells the glucose 6-phosphatase gene-promoter sequence from -161 to -152 is a cAMP response element which is important for the regulation of transcription of the glucose 6-phosphatase gene by both cAMP and glucocorticoids. (+info)

Analysis of 4-phosphopantetheinylation of polyhydroxybutyrate synthase from Ralstonia eutropha: generation of beta-alanine auxotrophic Tn5 mutants and cloning of the panD gene region. (4/4818)

The postulated posttranslational modification of the polyhydroxybutyrate (PHA) synthase from Ralstonia eutropha by 4-phosphopantetheine was investigated. Four beta-alanine auxotrophic Tn5-induced mutants of R. eutropha HF39 were isolated, and two insertions were mapped in an open reading frame with strong similarity to the panD gene from Escherichia coli, encoding L-aspartate-1-decarboxylase (EC 4.1.1.15), whereas two other insertions were mapped in an open reading frame (ORF) with strong similarity to the NAD(P)+ transhydrogenase (EC 1.6.1.1) alpha 1 subunit, encoded by the pntAA gene from Escherichia coli. The panD gene was cloned by complementation of the panD mutant of R. eutropha Q20. DNA sequencing of the panD gene region (3,312 bp) revealed an ORF of 365 bp, encoding a protein with 63 and 67% amino acid sequence similarity to PanD from E. coli and Bacillus subtilis, respectively. Subcloning of only this ORF into vectors pBBR1MCS-3 and pBluescript KS- led to complementation of the panD mutants of R. eutropha and E. coli SJ16, respectively. panD-encoded L-aspartate-1-decarboxylase was further confirmed by an enzymatic assay. Upstream of panD, an ORF with strong similarity to pntAA from E. coli, encoding NAD(P)+ transhydrogenase subunit alpha 1 was found; downstream of panD, two ORFs with strong similarity to pntAB and pntB, encoding subunits alpha 2 and beta of the NAD(P)+ transhydrogenase, respectively, were identified. Thus, a hitherto undetermined organization of pan and pnt genes was found in R. eutropha. Labeling experiments using one of the R. eutropha panD mutants and [2-14C]beta-alanine provided no evidence that R. eutropha PHA synthase is covalently modified by posttranslational attachment of 4-phosphopantetheine, nor did the E. coli panD mutant exhibit detectable labeling of functional PHA synthase from R. eutropha. (+info)

An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. (5/4818)

Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite the prokaryotic cell and genome organization, basal transcriptional elements of members of the domain Archaea (i.e., TATA box-like sequences, RNA polymerase, and transcription factors TBP, TFIIB, and TFIIS) are of the eukaryotic type. However, open reading frames potentially coding for bacterium-type transcription regulation factors have been recognized in different archaeal strains. This finding raises the question of how bacterial and eukaryotic elements interact in regulating gene expression in Archaea. We have identified a gene coding for a bacterium-type transcription factor in the hyperthermophilic archaeon Sulfolobus solfataricus. The protein, named Lrs14, contains a potential helix-turn-helix motif and is related to the Lrp-AsnC family of regulators of gene expression in the class Bacteria. We show that Lrs14, expressed in Escherichia coli, is a highly thermostable DNA-binding protein. Bandshift and DNase I footprint analyses show that Lrs14 specifically binds to multiple sequences in its own promoter and that the region of binding overlaps the TATA box, suggesting that, like the E. coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus. (+info)

Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. (6/4818)

The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes. (+info)

A binding site for homeodomain and Pax proteins is necessary for L1 cell adhesion molecule gene expression by Pax-6 and bone morphogenetic proteins. (7/4818)

The cell adhesion molecule L1 regulates axonal guidance and fasciculation during development. We previously identified the regulatory region of the L1 gene and showed that it was sufficient for establishing the neural pattern of L1 expression in transgenic mice. In the present study, we characterize a DNA element within this region called the HPD that contains binding motifs for both homeodomain and Pax proteins and responds to signals from bone morphogenetic proteins (BMPs). An ATTA sequence within the core of the HPD was required for binding to the homeodomain protein Barx2 while a separate paired domain recognition motif was necessary for binding to Pax-6. In cellular transfection experiments, L1-luciferase reporter constructs containing the HPD were activated an average of 4-fold by Pax-6 in N2A cells and 5-fold by BMP-2 and BMP-4 in Ng108 cells. Both of these responses were eliminated on deletion of the HPD from L1 constructs. In transgenic mice, deletion of the HPD from an L1-lacZ reporter resulted in a loss of beta-galactosidase expression in the telencephalon and mesencephalon. Collectively, our experiments indicate that the HPD regulates L1 expression in neural tissues via homeodomain and Pax proteins and is likely to be a target of BMP signaling during development. (+info)

Functional analysis of the promoter of the yeast SNQ2 gene encoding a multidrug resistance transporter that confers the resistance to 4-nitroquinoline N-oxide. (8/4818)

The yeast gene SNQ2, which encodes a multidrug resistance ABC superfamily protein, is required for resistance to the mutagen 4-nitroquinoline N-oxide (4-NQO). The expression of the SNQ2 gene is under the control of a regulatory network that involves the transcription factor Yrr1p, as well as Pdr1p/Pdr3p (Cui et al., Mol. Microbiol., 29, 1307-1315 (1998)). By 5'-deletion analysis of the promoter by using SNQ2-lacZ fusion constructs, four regions: -745 to -639 (region I), -639 to -578 (region II), -548 to -533 (region III) and -533 to -485 (region IV) were found to be important for SNQ2 expression. Genetic analysis suggested that the site in region IV was responsible for the Yrr1p-mediated SNQ2 expression. A consensus motif known for the binding of Pdr1p/Pdr3p (PDRE) was not found in region IV. (+info)

... can also be considered as consensus sequences. Thus a consensus sequence is a model for a putative DNA binding site: it is ... The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are ... Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as ... A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several ...

https://en.wikipedia.org/wiki/Consensus_sequence

The Kozak consensus sequence is so common that the similarity of the sequence around the AUG codon to the Kozak Sequence is ... The Kozak consensus sequence (Kozak consensus or Kozak sequence) is a nucleic acid motif that functions as the protein ... Kozak discovered the sequence through a detailed analysis of DNA genomic sequences. The Kozak sequence is not to be confused ... Kozak sequence, and leaderless initiation. Haloarchaea are known to have a variant of the Kozak consensus sequence in their ...

https://en.wikipedia.org/wiki/Kozak_consensus_sequence

... restriction sites can be generally represented by consensus sequences. This is because they target mostly identical sequences ... This makes it difficult to accurately represent transcription factor binding sites using consensus sequences, and they are ... Schneider T.D. (2002). "Consensus sequence Zen". Applied Bioinformatics. 1 (3): 111-119. PMC 1852464. PMID 15130839. Bulyk M.L ... can be represented by a consensus sequence. This representation has the advantage of being compact, but at the expense of ...

https://en.wikipedia.org/wiki/DNA_binding_site

... and T for each row should be equal because the PFM is derived from aggregating several consensus sequences. The sequence motif ... Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence ... a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be ... See also consensus sequence. Consider the N-glycosylation site motif mentioned above: Asn, followed by anything but Pro, ...

https://en.wikipedia.org/wiki/Sequence_motif

A common start site is defined within Kozak consensus sequence: (GCC) GCCACCAUGG in vertebrates. The sequence in brackets (GCC ... Exact nucleotide sequence and protein sequence of the specific coding sequence are also displayed in the section of CCDS ... The Consensus Coding Sequence (CCDS) Project is a collaborative effort to maintain a dataset of protein-coding regions that are ... There are variations within Kozak consensus sequence, such as G or A is observed three nucleotides upstream (at position -3) of ...

https://en.wikipedia.org/wiki/Consensus_CDS_Project

canonical sequence See consensus sequence. carboxyl terminus See C-terminus. carrier An individual who has inherited a ... insertion sequence (IS) Any nucleotide sequence that is inserted naturally or artificially into another sequence. The term is ... consensus sequence A calculated order of the most frequent residues (of either nucleotides or amino acids) found at each ... in-frame 1. (of a gene or sequence) Read or transcribed in the same reading frame as another gene or sequence; not requiring a ...

https://en.wikipedia.org/wiki/Glossary_of_genetics_(0–L)

"Report for CCDS2297.1". Consensus Coding Sequence (CDS) Database. National Center for Biotechnology Information (NCBI). Byers, ... June 1993). "Sequencing of cDNA from 50 unrelated patients reveals that mutations in the triple-helical domain of type III ... This (Gly-X-Y)n sequence is repeated 343 times in the type III collagen molecule. Proline or hydroxyproline is often found in ... June 2015). "Vascular Ehlers-Danlos Syndrome in siblings with biallelic COL3A1 sequence variants and marked clinical ...

https://en.wikipedia.org/wiki/Collagen,_type_III,_alpha_1

Nuclear targeting sequences-a consensus?. Trends in biochemical sciences. 1991 Jan 1;16:478-81. According to Google Scholar, ... Dingwall C, Laskey RA (December 1991). "Nuclear targeting sequences--a consensus?". Trends in Biochemical Sciences. 16 (12): ... Detailed mapping of the sequence in nucleoplasmin revealed a longer sequence motif within which two domains of basic amino ... nuclear localization sequence has emerged as the major nuclear localization sequence in cellular proteins and the sequence ...

https://en.wikipedia.org/wiki/Colin_Dingwall

Dingwall C, Laskey RA (December 1991). "Nuclear targeting sequences - a consensus?". Trends Biochem. Sci. 16 (12): 478-81. doi: ... Glu sequence, nor in the positions immediately flanking this sequence. The pRb-binding motif and negatively charged region ... The NLS sequence is PKKKRKV. SV40 large TAg, other polyomavirus large T antigens, adenovirus E1a proteins, and oncogenic human ... Figge J, Smith TF (14 July 1988). "Cell division sequence motif". Nature. 334 (6178): 109. doi:10.1038/334109a0. PMID 3290690. ...

https://en.wikipedia.org/wiki/SV40_large_T_antigen

proposed the consensus sequence K-K/R-X-K/R for monopartite NLSs. A Chelsky sequence may, therefore, be part of the downstream ... Dingwall C, Laskey RA (December 1991). "Nuclear targeting sequences--a consensus?". Trends in Biochemical Sciences. 16 (12): ... A nuclear localization signal or sequence (NLS) is an amino acid sequence that 'tags' a protein for import into the cell ... The first NLS to be discovered was the sequence PKKKRKV in the SV40 Large T-antigen (a monopartite NLS). The NLS of ...

https://en.wikipedia.org/wiki/Nuclear_localization_sequence

canonical sequence See consensus sequence. carboxyl terminus See C-terminus. carrier An individual who has inherited a ... sequence See nucleic acid sequence. sequence-tagged site (STS) Any DNA sequence that occurs exactly once within a particular ... palindromic sequence A nucleic acid sequence of a double-stranded DNA or RNA molecule in which the unidirectional sequence (e.g ... Sanger sequencing A method of DNA sequencing based on the in vitro replication of a DNA template sequence, during which ...

https://en.wikipedia.org/wiki/Glossary_of_genetics

It has the consensus sequence GACCACCCAC. The individual zinc finger motifs are separated from one another by the amino acid ... to interact with target DNA sequences to regulate gene transcription. The domain interacts sequence specifically with the DNA, ... The protein's termini are fairly unusual, and have no strong sequence similarity other proteins. Glis1 can be used as one of ... a change in a single nucleotide of the DNA sequence of the gene, has been implicated as a risk factor in the neurodegenerative ...

https://en.wikipedia.org/wiki/GLIS1

B) The consensus sequence of Ter. [3] The Ter sites specifically interact with the replication terminator protein called Tus in ... a 9-mer repeat with a highly conserved consensus sequence 5' - TTATCCACA - 3', that are recognized by the DnaA protein. DnaA ... Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52 ... The E. coli bacterial replication origin, called oriC consists of DNA sequences that are recognised by the DnaA protein, which ...

https://en.wikipedia.org/wiki/Circular_chromosome

SOAPsnp is a consensus sequence builder. This tool uses the output from SOAPaligner to generate a consensus sequence which ... and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data. All programs in ... 2009). "The sequence and de novo assembly of the giant panda genome". Nature. 463 (7279): 311-317. doi:10.1038/nature08696. ... The first release of SOAP consisted only of the sequence alignment tool SOAPaligner. SOAP v2 extended and improved on SOAP v1 ...

https://en.wikipedia.org/wiki/Short_Oligonucleotide_Analysis_Package

The quality of the alignment determines the accuracy of the consensus structure model. Consensus sequences are folded using ... Chiu D.K.; Kolodziejczak T. (1991). "Inferring consensus structure from nucleic acid sequences". Comput. Appl. Biosci. 7 (3): ... Sequence covariation methods rely on the existence of a data set composed of multiple homologous RNA sequences with related but ... A less widely used approach is to fold the sequences using single sequence structure prediction methods and align the resulting ...

https://en.wikipedia.org/wiki/Nucleic_acid_structure_prediction

... single-strand consensus sequences (SSCS) and duplex consensus sequences (DCS) assembly. Duplex sequencing theoretically can ... A consensus sequence is then generated for each family using the identical sequences in each position of the remaining reads. ... The remaining reads are assembled to consensus sequences using SSCS and DCS assemblies. Trimmed sequences from the previous ... The consensus sequence is called the SSCS. It increases the NGS accuracy to about 20 fold higher; however, this method relies ...

https://en.wikipedia.org/wiki/Duplex_sequencing

... terminal 16S rRNA sequence can restore translation. Kozak consensus sequence, the sequence that targets the ribosome to the ... The six-base consensus sequence is AGGAGG; in Escherichia coli, for example, the sequence is AGGAGGU, while the shorter GAGG ... Given the complementary relationship between rRNA and the Shine-Dalgarno sequence in mRNA, it was proposed that the sequence at ... The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome ...

https://en.wikipedia.org/wiki/Shine–Dalgarno_sequence

Christoffels A, van Gelder A, Greyling G, Miller R, Hide T, Hide W (Jan 2001). "STACK: Sequence Tag Alignment and Consensus ... In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene ... Because of the way ESTs are sequenced, many distinct expressed sequence tags are often partial sequences that correspond to the ... Alternatively, if the genome of the organism that originated the EST has been sequenced, one can align the EST sequence to that ...

https://en.wikipedia.org/wiki/Expressed_sequence_tag

SELEX: Employed to determine consensus binding sequences. Competition-ChIP: Measures relative replacement dynamics on DNA. ... ChIL sequencing (ChIL-seq), also known as Chromatin Integration Labeling sequencing, is a method used to analyze protein ... Sequencing of prepared DNA libraries and comparison to whole-genome sequence databases allows researchers to analyze the ... ChIL-sequencing combines antibody-targeted controlled cleavage by Tn5 transposase with massively parallel DNA sequencing to ...

https://en.wikipedia.org/wiki/ChIL-sequencing

SELEX: Employed to determine consensus binding sequences. Competition-ChIP: Measures relative replacement dynamics on DNA. ... Sensitivity of sequencing depends on the depth of the sequencing run (i.e. the number of mapped sequence tags), the size of the ... Sequencing of prepared DNA libraries and comparison to whole-genome sequence databases allows researchers to analyze the ... The data is then collected and analyzed using software that aligns sample sequences to a known genomic sequence to identify the ...

https://en.wikipedia.org/wiki/CUT&Tag_sequencing

... the consensus around this sequence varies somewhat. In humans the branch site consensus sequence is yUnAy. The branch site is ... The typical eukaryotic nuclear intron has consensus sequences defining important regions. Each intron has the sequence GU at ... The intron upstream from exon 4 has a polypyrimidine tract that doesn't match the consensus sequence well, so that U2AF ... Gao K, Masuda A, Matsuura T, Ohno K (April 2008). "Human branch point consensus sequence is yUnAy". Nucleic Acids Research. 36 ...

https://en.wikipedia.org/wiki/Alternative_splicing

https://en.wikipedia.org/wiki/CUT&RUN_sequencing

Eddy, S. R.; Mitchison, G; Durbin, R (1995). "Maximum discrimination hidden Markov models of sequence consensus". Journal of ... c. Elegans Sequencing, C. (1998). "Genome sequence of the nematode C. Elegans: A platform for investigating biology". Science. ... More recently Durbin has returned to sequencing and has developed low coverage approaches to population genome sequencing, ... Birney, Ewan (2000). Sequence alignment in bioinformatics. cam.ac.uk (PhD thesis). University of Cambridge. OCLC 894597337. ...

https://en.wikipedia.org/wiki/Richard_M._Durbin

Nevertheless, PRMTs with non-GAR consensus sequences exist. PRMTs are present in the nucleus as well as in the cytoplasm. In ... Proteins containing the consensus motif H2N-X-Pro-Lys- (where X can be Ala, Pro or Ser) after removal of the initiator ...

https://en.wikipedia.org/wiki/Protein_methylation

The G5 motif contains a SAK consensus sequence. The A is alanine146, which provides specificity for guanine rather than adenine ... Dynamic electrostatic interactions between its positively charged basic sequence with negative charges at the inner leaflet of ... or the combination of prenylation and a polybasic sequence adjacent to the prenylation site (KRAS). The C-terminal CaaX box of ...

https://en.wikipedia.org/wiki/Ras_GTPase

The consensus sequence of Inr in humans was inferred to be YYANWYY. The consensus sequence in Drosophila is TCAKTY. Studies ... It has the consensus sequence YYANWYY in humans. Similarly to the TATA box, the Inr element facilitates the binding of ... Out of those sequences with the TATA box, 62% contained the Inr element as well. Though the Inr element is not fully understood ... This sequence encompasses where the RNA polymerase will begin transcribing. The Inr element is located about ~20 bp downstream ...

https://en.wikipedia.org/wiki/Initiator_element

"Novel consensus DNA-binding sequence for BRCA1 protein complexes". Mol. Carcinog. 38 (2): 85-96. doi:10.1002/mc.10148. PMID ... When this happens, it is difficult for the repair mechanism to "know" how to replace the correct DNA sequence, and there are ... Zheng L, Pan H, Li S, Flesken-Nikitin A, Chen PL, Boyer TG, Lee WH (October 2000). "Sequence-specific transcriptional ... Classical methods for mutation detection (sequencing) are unable to reveal these types of mutation. Other methods have been ...

https://en.wikipedia.org/wiki/BRCA1

They have the consensus amino acid sequence of RPNVELCRD. Different types of tektins, designated as A (53 kDa), B (51 kDa), C ( ... Amino acid sequences of tektins are well conserved, with significant similarity between mouse and human homologs. Tubulin ... The 2 segments are similar in sequence, indicating a gene duplication event. Along each tektin rod, cysteine residues occur ...

https://en.wikipedia.org/wiki/Tektin

No consensus sequence for protein palmitoylation has been identified. Palmitoylated proteins are mainly found on the ... In the CaaX box sequence, the C represents the cysteine that is prenylated, the A represents any aliphatic amino acid and the X ... This reaction is facilitated by N-myristoyltransferase . These proteins usually begin with a Met-Gly sequence and with either a ...

https://en.wikipedia.org/wiki/Lipid-anchored_protein

For multiple sequences the last row in each column is often the consensus sequence determined by the alignment; the consensus ... Sequenced RNA, such as expressed sequence tags and full-length mRNAs, can be aligned to a sequenced genome to find where there ... Schneider TD; Stephens RM (1990). "Sequence logos: a new way to display consensus sequences". Nucleic Acids Res. 18 (20): 6097- ... Sequence homology Sequence mining BLAST String searching algorithm Alignment-free sequence analysis UGENE Needleman-Wunsch ...

https://en.wikipedia.org/wiki/Sequence_alignment

The site's consensus reads, "Favoring garish style over effective storytelling, the fifth American Horror Story strands a ... Same day the title sequence of the season was released by Murphy, consisting of the same soundtrack like previous seasons, ... Woerner, Meredith (October 1, 2015). "'American Horror Story: Hotel' title sequence is a germaphobe's nightmare". Los Angeles ... Bryant, Jacob (October 1, 2015). "Watch: 'American Horror Story: Hotel' Opening Sequence Gets Biblical". Variety. Archived from ...

https://en.wikipedia.org/wiki/American_Horror_Story:_Hotel

ISBN 978-1-4669-3935-6. Russell, Andrew L. (July-September 2006). "'Rough Consensus and Running Code' and the Internet-OSI ... independently of other packets whereas a connection-oriented virtual circuit transports packets between terminals in sequence. ...

https://en.wikipedia.org/wiki/Protocol_Wars

Isolated from Tempe based on Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR)". HAYATI ... DNA sequence and mechanism of transfer". Journal of Bacteriology. 182 (1): 81-90. doi:10.1128/jb.182.1.81-90.2000. PMC 94243. ...

https://en.wikipedia.org/wiki/Antonius_Suwanto

The website's consensus reads, "Pirates of the Caribbean: Dead Men Tell No Tales proves that neither a change in directors nor ... and Bruckheimer had previously mentioned that there might be a sequence in Louisiana. However, a spokesman for Australian Arts ...

https://en.wikipedia.org/wiki/Pirates_of_the_Caribbean:_Dead_Men_Tell_No_Tales

Hooton, Christopher (January 23, 2017). "Game of Thrones season 7: Bastille 'film cameo in battle sequence'". The Independent. ... with the site's consensus reading, "After a year-long wait, Game of Thrones roars back with powerful storytelling and a focused ...

https://en.wikipedia.org/wiki/Game_of_Thrones_(season_7)

... which have a highly conserved 9 bp consensus sequence 5' - TTATC/ACACA ) are high affinity DnaA boxes. They bind to DnaA-ADP ... These sequences allow the two replication forks to pass through in only one direction, but not the other. DNA replication ... In E. coli, the direction for orisome assembly are built into a short stretch of nucleotide sequence called as origin of ... Termination of DNA replication in E. coli is completed through the use of termination sequences and the Tus protein. ...

https://en.wikipedia.org/wiki/Prokaryotic_DNA_replication

In the end, the determining factor was just plain strakhfulness and consensus.) The head of a Great Family was considered a ... The Slobbovians justified their conquest by reversing the sequence.] The latter, ruled by the Rabinsky family, were held to be ...

https://en.wikipedia.org/wiki/Slobbovia

The site's consensus states: "Angelina Jolie conveys the full emotional range of a woman in a desperate situation in A Mighty ... The production also shot multiple scenes in Austin, Texas in early 2007, including a key sequence with Marianne Pearl giving an ...

https://en.wikipedia.org/wiki/A_Mighty_Heart_(film)

99-100), following his teacher Eugen Ewig, believes that the exile story reflects a real sequence of events whereby Childeric ... there is no consensus on this, because the reference in this case is not apparently to events near the Loire.[citation needed] ... gives a sequence of events which are very difficult to interpret. In 463 Childeric and Aegidius successfully repelled the ...

https://en.wikipedia.org/wiki/Childeric_I

There is no current consensus and 3-planet, 4-planet, 5-planet and 6-planet models have been proposed to address the available ... M-type main-sequence stars, BY Draconis variables, Objects with variable star designations, Durchmusterung objects, Libra ( ... The planet remained unconfirmed as consensus for its existence could not be reached. Additional reanalysis only found evidence ... was at the time the least massive confirmed exoplanet identified around a main-sequence star. On 29 September 2010, astronomers ...

https://en.wikipedia.org/wiki/Gliese_581

Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials. Molecular Phylogenetics and Evolution ... reflecting the consensus of older studies, Archer et al. (2011) report the presence of four molars (typical for marsupials) in ... An analysis of marsupial interordinal relationships based on 12S rRNA, tRNA valine, 16S rRNA, and cytochrome b sequences. ... Phillips MJ, McLenachan PA, Down C, Gibb GC, Penny D. Combined mitochondrial and nuclear DNA sequences resolve the ...

https://en.wikipedia.org/wiki/Marsupial_mole

"NIH Consensus Statement on Management of Hepatitis C: 2002". NIH Consensus and State-Of-The-Science Statements. 19 (3): 1-46. ... Zoon KC, Smith ME, Bridgen PJ, Anfinsen CB, Hunkapiller MW, Hood LE (February 1980). "Amino terminal sequence of the major ... Inside the nucleus, the ISGF3 complex binds to specific nucleotide sequences called IFN-stimulated response elements (ISREs) in ... amino acid analysis and amino terminal amino acid sequence". Science. 207 (4430): 525-6. Bibcode:1980Sci...207..525K. doi: ...

https://en.wikipedia.org/wiki/Interferon

... order sequence, etc.[citation needed] Finished tasks can also be foreseen with the report, showing what exactly has been done ... ", "fixed", or a group consensus that the issue is not worth solving, such as "not a problem" or "won't fix"); that each issue ...

https://en.wikipedia.org/wiki/Issue_tracking_system

There is no consensus on an appropriate treatment approach of esthesioneuroblastoma because of the rarity of the disease. Most ... 2012). "Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma". PLOS ONE. 7 (5): e37029. ...

https://en.wikipedia.org/wiki/Esthesioneuroblastoma

... though the general consensus appears to be that they are non-placental eutherians and that there are non known Cretaceous ... inferred from mitochondrial rRNA gene sequences, Department of Zoology, The Natural History Museum, London SW7 5BD, UK b ...

https://en.wikipedia.org/wiki/Insular_India

Depending on the nature and position of each mutation, a consensus significant loss of betasheet structure of the Notch3 ... The definitive test is sequencing the whole Notch 3 gene, which can be done from a sample of blood. However, as this is quite ...

https://en.wikipedia.org/wiki/CADASIL

... has the consensus sequence TATAAT. The sequence at -35 (the -35 element) has the consensus sequence TTGACA. The above consensus ... consensus sequence 5'-AAAAAARNR-3' when centered in the -42 region; consensus sequence 5'-AWWWWWTTTTT-3' when centered in the - ... Promoter DNA sequences provide an enzyme binding site. The -10 sequence is TATAAT. -35 sequences are conserved on average, but ... we may call the most common sequence in a population the wild-type sequence. It may not even be the most advantageous sequence ...

https://en.wikipedia.org/wiki/Promoter_(genetics)

Tournament mode sees the player attempt to complete a number of courses in sequence, trying to achieve a fast overall time with ... Gallegos, Anthony (2009-08-12). "The Consensus: Trials HD Review". GameSpy. IGN Entertainment. Retrieved 2010-10-13. "Trials HD ...

https://en.wikipedia.org/wiki/Trials_HD

The site's critical consensus states: "Children of Men works on every level: as a violent chase thriller, a fantastical ... Children of Men used several lengthy single-shot sequences in which extremely complex actions take place. The longest of these ... In an interview with Variety, Cuarón acknowledged this nature of the "single-shot" action sequences: "Maybe I'm spilling a big ... Debruge, Peter (19 February 2007). "Editors cut us in on tricky sequences". Variety. Wagner, Annie (28 December 2006). " ...

https://en.wikipedia.org/wiki/Children_of_Men

The site's consensus states: "Hairspray is an energetic, wholly entertaining musical romp; a fun Summer movie with plenty of ... A PCC streetcar with Toronto Transit Commission livery is seen in the opening sequence. Some of the signs for the 1960s-era ... in that great sequence in Funny Girl. Shankman, Adam (July 25, 2007). "The Director's Chair: Adam Shankman's Hairspray Diary # ... Shankman based Edna's dancing style on the hippo ballerinas in the Dance of the Hours sequence in Walt Disney's 1940 animated ...

https://en.wikipedia.org/wiki/Hairspray_(2007_film)

The sequence where the crew is pursued by Reavers after a bank robbery was filmed along the Templin Highway north of Santa ... The site's critical consensus states: "Snappy dialogue and goofy characters make this Wild Wild West soap opera in space fun ... The videos, sequenced out of chronological order, depict excerpts of counseling sessions between River Tam, played by Summer ... The shoot typically would have lasted 30 days, but the production completed filming the sequence in five days. Pyrotechnics ...

https://en.wikipedia.org/wiki/Serenity_(2005_film)

"Copenhagen Consensus Center". Retrieved 30 August 2014. Raulin J (1869). "Chemical studies on vegetation". Annales des Sciences ... Animal studies indicate that maternal zinc deficiency can upset both the sequencing and efficiency of the birth process. An ... to humans is one of the four solutions to major global problems identified in the Copenhagen Consensus from an international ...

https://en.wikipedia.org/wiki/Zinc_deficiency

Molecular studies over the past 30 years have led to a wide consensus that Darwin was correct, with studies showing that ... and matK DNA sequences", American Journal of Botany, 89 (1): 132-144, doi:10.3732/ajb.89.1.132, PMID 21669721 Albert, V. A.; ... based on chloroplast rbcL and nuclear 18S ribosomal DNA Sequences". American Journal of Botany. 90 (1): 123-130. doi:10.3732/ ... a cladistic analysis of rbcL sequence and morphological data", American Journal of Botany, 81 (8): 1027-1037, doi:10.2307/ ...

https://en.wikipedia.org/wiki/Droseraceae

The flashback sequences featuring a younger Hank Pym were set around the same time as the flashback sequences of Ant-Man, so ... The website's critical consensus reads, "A lighter, brighter superhero movie powered by the effortless charisma of Paul Rudd ... The film's main credits sequence is a "table-top" version of its action sequences, and was created by Elastic. An alternative ... Eric Eisenberg of Cinema Blend opined that a standalone adventure with Pym and the cut sequence would be a good candidate to ...

https://en.wikipedia.org/wiki/Ant-Man_and_the_Wasp

Ulam's work on non-Euclidean distance metrics in the context of molecular biology made a significant contribution to sequence ... After extensive discussion, the participants reached a consensus that his ideas were worthy of further exploration. A few weeks ... Goad, Walter B (1987). "Sequence Analysis: Contributions of Ulam to Molecular Genetics" (PDF). Los Alamos Science. Los Alamos ... challenged conclusions of Walter by writing that Ulam had only modest influence on early development of sequence alignment ...

https://en.wikipedia.org/wiki/Stanislaw_Ulam

Ewen, Callaway (22 September 2011). "First Aboriginal genome sequenced". Nature News. doi:10.1038/news.2011.551. Bocquet-Appel ... societies may have made decisions by communal consensus decision making rather than by appointing permanent rulers such as ...

https://en.wikipedia.org/wiki/Paleolithic

conifers) (1) Gymnosperm (Acrogymnospermae) taxonomy has been considered controversial, and lacks consensus. As taxonomic ... Evidence from rbcL Sequences". Systematic Botany. 19 (2): 253. doi:10.2307/2419600. JSTOR 2419600. Chamberlain, Charles Joseph ... with the intention of reaching a consensus. Gymnosperms form a group of four subclasses among the spermatophytes (seed bearing ... "A new classification and linear sequence of extant gymnosperms" (PDF). Phytotaxa. 19 (1): 55-70. doi:10.11646/phytotaxa.19.1.3 ...

https://en.wikipedia.org/wiki/Pinales

There is still not a consensus among biologists that the American and Chinese alligators belong to the same genus, despite ... Wu, Ziaobang; Zhou, Kaiya; Wang, Yiquan; Zhu, Weiquan (October 2003). "Complete mitochondrial DNA sequence of Chinese alligator ... "Complete mitochondrial DNA sequence of Chinese alligator, Alligator sinensis, and phylogeny of crocodiles". Chinese Science ...

https://en.wikipedia.org/wiki/Chinese_alligator

The website's consensus reads, "A gleefully gonzo franchise revival, Jackass Forever will make you worry more than ever for the ... Dave England also burnt his right hand during the opening sequence. Zach Holmes got an infection after he glided into the ... producer Spike Jonze's father Lionel Boyce Cameos in the intro sequence include Arthur H. Spiegel III, Errol Chatham, Alia ...

https://en.wikipedia.org/wiki/Jackass_Forever

... sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and ... previously developed guidance for the interpretation of sequence variants.(1) In the past decade, ... Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College ... sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and ...

https://pubmed.ncbi.nlm.nih.gov/25741868/?dopt=Abstract

... for a multiply aligned set of sequences (Seqs), returns a character vector with the consensus sequence (CSeq). ... for a multiply aligned set of sequences (. Seqs. ), returns a character vector with the consensus sequence (. CSeq. ). The ... returns a character vector with the consensus sequence (. CSeq. ) from a sequence profile (. Profile. ). ... Sequence. .. Profile. Sequence profile. Enter a profile from the function seqprofile. . Profile. is a matrix of size [20 (or 4 ...

https://es.mathworks.com/help/bioinfo/ref/seqconsensus.html

... Files from the Illumina MiSeq and HiSeq 2500 sequencing runs were ... Consensus mtDNA genome sequences for each sample were constructed using the Samtools mpileup command with the -C50 parameter to ... We required minimums of 2X non-redundant sequence coverage and 80% site identity per site for consensus base calling ... processed as described (see description for Puma concolor Mitochondrial DNA Sequence Files from Illumina HiSeq 2500/MiSeq ...

https://scholarsphere.psu.edu/resources/1cc01c27-6665-42ef-be2e-cf2cd24741ec

... return self.sequence_string[(self.sequence_string.index(val) + 1) % len(self.sequence_string)] # # Simple Sequence Functions # ... sequence_string self.sequence_length = len(sequence_string[0]) self.rollover = rollover self.last_item = sequence_string[-1] ... self.sequence_length: return self.sequence_string[0] last_value = val[-self.sequence_length:] if (not self.rollover) and (last_ ... param sequence_string: The string or list that explains how to generate the next item in the sequence :type sequence_string: ...

https://toolshed.g2.bx.psu.edu/repos/shellac/sam_consensus_v3/file/tip/env/lib/python3.9/site-packages/boto/sdb/db/sequence.py

Convergent Solid-Phase Synthesis of N-Glycopeptides Facilitated by Pseudoprolines at Consensus-Sequence Ser/Thr Residues. In: ... Convergent Solid-Phase Synthesis of N-Glycopeptides Facilitated by Pseudoprolines at Consensus-Sequence Ser/Thr Residues ...

https://eref.uni-bayreuth.de/5565/

Macro-haplogroup consensus sequences reliability. Based on the hypothesis that the mtDNA variants spread and fixed in one or ... Macro-haplogroup consensus sequences (MHCS) phylogeny. The robustness of 32 MHCSs was tested by generating a phylogenetic tree ... The consistency of MHCSs as consensus is supported by the clustering of such sequences with real genomes belonging to the same ... 2013). In this context, we used the Macro Haplogroup Consensus Sequences to move the fixed evolutionary variants to the ...

https://link.springer.com/article/10.1007/s00439-015-1615-9

I would like to determine consensus sequences in unaligned reads. I know that the usual way is to first align them to a ... I would like to determine consensus sequences in unaligned reads. I know that the usual way is to first align them to a ... Generating consensus sequences from unaligned reads 09-06-2022, 06:08 AM. ...

https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/322362-generating-consensus-sequences-from-unaligned-reads

Perform protein alignments from Template You can use our protein alignment tool to perform consensus alignments for proteins or ... Name your Consensus AA Sequencing, save it in a folder and click on "Create Alignment." ... How can I see all alignments Ive performed with a protein sequence?. Open your DNA or amino acid sequence. Click on the ... button to designate the AA sequence as your template. To change the template AA sequence, simply click on "Unset Template." ...

https://help.benchling.com/hc/en-us/articles/9684279510413-Perform-consensus-or-template-alignments-on-protein-sequences

Rapid Sequence Induction (RSI) was introduced to minimise the risk of aspiration of gastric contents during emergency tracheal ... Avery, P., Morton, S., Raitt, J. et al. Rapid sequence induction: where did the consensus go?. Scand J Trauma Resusc Emerg Med ... Rapid sequence induction: where did the consensus go?. *Pascale Avery. ORCID: orcid.org/0000-0002-0110-04121, ... Rapid Sequence Induction (RSI) was introduced to minimise the risk of aspiration of gastric contents during emergency tracheal ...

https://sjtrem.biomedcentral.com/articles/10.1186/s13049-021-00883-5

Being Poland syndrome a rare syndrome most recommendations here presented are good clinical practice based on the consensus of ... books and guidelines were reviewed and final recommendations were reached by consensus. ... Consensus based recommendations for diagnosis and medical management of Poland syndrome (sequence). Access & Citations. * 8735 ...

https://ojrd.biomedcentral.com/articles/10.1186/s13023-020-01481-x/metrics

Consensus Sequence. Blum CA, Tanaka T, Zhong X, Li Q, Dashwood W-M, Pereira C, Xu M, Dashwood RH. 2003. Mutational analysis of ... Base Sequence. Blum CA, Tanaka T, Zhong X, Li Q, Dashwood W-M, Pereira C, Xu M, Dashwood RH. 2003. Mutational analysis of ...

https://lpi.oregonstate.edu/biblio?f%5Bauthor%5D=6216&o=asc&page=29&s=keyword

include consensus sequence. ?. Format:. Hypertext. Plain Text. mFasta. Compact Hypertext. Compact Text. Row Display:. Color ...

https://www.ncbi.nlm.nih.gov/Structure/cdd/TIGR02250

... but also provides basic statistics of the CRISPR sequences, and the consensus sequences of DRs/spacers across the input strains ... CrisprVi is a convenient tool for visualizing and analyzing the CRISPR sequences and it would be helpful for users to inspect ... orders and components of the CRISPR sequences in a global view. In comparison to other CRISPR visualization tools such as ... label and align the CRISPR sequences, which help researchers investigate the locations, ...

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04716-9

... and profile sequence alignments using dynamic programming algorithms; BLAST searches and alignments; standard and custom ... Calculate consensus sequence. seqprofile. Calculate sequence profile from set of multiply aligned sequences. ... Compare Sequences Using Sequence Alignment Algorithms. Determining the similarity between two sequences is a common task in ... Sequence Alignments. You can select from a list of analysis methods to compare nucleotide or amino acid sequences using ...

https://www.mathworks.com/help/bioinfo/sequence-alignment.html

The reported ICP4 consensus sequence42,60,61 was used as positive control; a G-rich non-folding sequence (scrambled, S) was ... In addition, HIV-1 LTR-III i-motif forming sequence (LTR-IIIc) and the reported ICP4 consensus sequence (IE3) were used as non- ... as well as the reported consensus sequence (Fig. 3a and Supplementary Fig. S10b): the two best bound sequences were ICP4-146532 ... IE-CS is the reported ICP4 consensus sequence42, 60, 61; SCR is a G-rich unfolded oligo; CTR is a control lane loaded with ...

https://www.nature.com/articles/s42003-021-02035-y?error=cookies_not_supported&code=8e82e0f5-f7c5-42ec-bc4b-6dfdc9aa6576

Table 4. Conserved motif sequence of Zea mays HSFs.. Motif. Consensus Sequence. ... Sequence Analysis. The coding sequence (CDS) and genomic DNA sequences were obtained from the maize genome database (MaizeGDB ... Sequence Alignment and Phylogenetic Analysis. The protein sequences of Arabidopsis thaliana, Oryza sativa, Brachypodium ... cis-regulatory region sequence-specific DNA binding (GO:0000987), RNA polymerase II transcription regulatory region sequence- ...

https://www.mdpi.com/2073-4395/11/11/2335

... build a consensus sequence from the reads Align the consensus sequences to a HLA-A sequence database to find the best match ... Single-Molecule Circular Consensus Sequence (CCS) and Multi-Molecule Consensus Single-Molecule CCS: Multi-Molecule Consensus: ... Test the Consensus Algorithm on HIV Data (~9 kb Amplicons) Difference between PacBio® Consensus vs. Sanger Assembly Consensus ... 2nd Generation Sequencing Can Help Resolve Ambiguities 28 If the SNPs that need to be phased are in the sequenced exons and ...

https://speakerdeck.com/pacbio/future-applications-phasing-and-sequencing-of-viral-mixtures

... and conquer processing algorithm for SMRT amplicon-sequence data that generates accurate consensus sequences and local sequence ... Pacific Biosciences generated unexpected numbers of amplicon sequences with substantial inaccuracies in the consensus sequences ... comprised of multiple low quality subreads from which higher quality circular consensus sequences are formed) to cluster raw ... C3S-LAA produced accurate consensus sequences and assemblies of overlapping amplicons from single sample and multiplexed ...

https://www.pacb.com/publications/clustering-of-circular-consensus-sequences-accurate-error-correction-and-assembly-of-single-molecule-real-time-reads-from-multiplexed-amplicon-libraries/

Their LRRs have a specific consensus pattern with characteristic differences from the previously described consensus sequences ... Their LRRs have a specific consensus pattern with characteristic differences from the previously described consensus sequences ...

https://www.dot1linhibitor.com/2017/04/24/their-lrrs-have-a-specific-consensus-pattern-with-characteristic-differences-from-the-previously-described-consensus-sequences-of-lrr-subfamilies/

SINE family of non-LTR retrotransposons - a consensus sequence. Submitted: 28-Mar-2010 Accepted: 28-MAR-2010 ... 96% identical to consensus. Shows 3 similarity to Ingi-type element. Several times more abundant than SINE-1_ACar.. ...

https://www.girinst.org/2010/vol10/issue4/SINE-1B_ACar.html

SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences ... Accurate consensus sequence from nanopore reads of a gene library. Bioconductor version: Release (3.16) ... Accurate consensus sequence from nanopore reads of a DNA gene library. ...

https://bioconductor.org/packages/release/bioc/html/single.html

The consensus coding sequences of human breast and colorectal cancers.. October 2, 2021. September 30, 2021. by Jose ... To start out a scientific analysis of such alterations, we determined the sequence of well-annotated human protein-coding genes ... The elucidation of the human genome sequence has made it potential to ascertain genetic alterations in cancers in unprecedented ...

https://www.ncbcs.org/tag/foxa2-antibody/

... including the handling of protein and peptide sequences, the visualization of (and in... ...

https://www.researchgate.net/profile/Kenny-Helsens

... to produce finalized consensus sequences.. We aligned our sequences and those available in GenBank (Table S1) using MUSCLE ( ... Finally, two mtDNA sequences from captive-bred P. aurotaenia of unknown origin (sequenced by Grant et al. [2006] and Santos et ... Meyer, M., & Kircher, M. (2010). Illumina sequencing library preparation for highly multiplexed target capture and sequencing. ... Sun, Y.-B., Xiong, Z.-J., Xiang, X.-Y., Liu, S.-P., Zhou, W.-W., Tu, X.-L.,…Zhang, Y.-P. (2015). Whole-genome sequence of the ...

https://www.biorxiv.org/content/10.1101/2020.02.21.960005v2.full

Consensus engineering of sucrose phosphorylase: the outcome reflects the sequence input Dirk Aerts (UGent) , Tom Verhaeghe ( ... Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis An ...

https://biblio.ugent.be/person/F9CBE36C-F0ED-11E1-A9DE-61C894A0A6B4

Consensus Sequence. Blum CA, Tanaka T, Zhong X, Li Q, Dashwood W-M, Pereira C, Xu M, Dashwood RH. 2003. Mutational analysis of ...

https://lpi.oregonstate.edu/biblio?page=4&f%5Bauthor%5D=3281&o=desc&s=keyword

... and consensus sequences representing each animal were created. These consensus sequences were deposited in GenBank under ... Sequences obtained were compared for similarity to sequences in GenBank by using the BLAST program (www.ncbi.nlm.nih.gov/BLAST ... This sequence was closest (99.5% identity over 222 bp) to L. infantum (Table). DNA sequences from all the positive tissues ... Sequences were compared with the following Leishmania sequences deposited in GenBank: L. tropica FJ595949 and FJ595950 from ...

https://wwwnc.cdc.gov/eid/article/16/12/10-0953_article

DNA encoding consensus TFBS sequences were inserted upstream of PTK. Fluc was then replaced with a unique DNA reporter sequence ... Oka, T., Rairkar, A., and Chen, J. H. (1991). Structural and functional analysis of the regulatory sequences of the ets-1 gene ... Transcription factor binding sites (TFBS) that are found in conserved non-coding sequences (CNS), taking into consideration ... Antibody for E26 transformation-specific sequence-1 (ETS1) detection was purchased from Novus Biologicals (Centennial, CO). ...

https://www.frontiersin.org/articles/10.3389/fphys.2021.683651/full

Sequences were aligned and a consensus sequence deduced for each species. A pair of oligonucleotides was designed in high ... Sequences of cytochrome oxidase subunit I (COI) gene from nine species of Diptera of forensic importance registered in GenBank ... was identified by sequencing internal transcribed spacer regions of ribosomal DNA (rDNA). Assays against immature sweetpotato ... we found the following sequence: Latin® , Peokubo® , Polar Star® , Leonidas® , Royal Bacara® , Haylander® , Ben Hur®. In ...

https://bioone.org/journals/southwestern-entomologist/volume-39/issue-4

GATA1 regulates its target genes through binding to consensus DNA sequence. GATA1 was first found critical for the formation of ... Primer sequences used were listed in Table S4b.. 2.9. Dual-Luciferase Reporter Assay. Cells were seeded into 24-well plates at ... Primer sequences used were listed in Table S4c.. 2.11. Flow Cytometry Assay. Cell apoptosis was analyzed using an Annexin V-APC ... Lentiviral vector of GATA1 was constructed by cloning PCR-amplified full length sequences into pCDH (System Biosciences). The ...

https://www.hindawi.com/journals/jo/2019/9474273/

Anatomy10

Organisms15

Diseases1

Chemicals and Drugs91

Analytical, Diagnostic and Therapeutic Techniques and Equipment35

Psychiatry and Psychology1

Phenomena and Processes105

Disciplines and Occupations1

Anthropology, Education, Sociology and Social Phenomena1

Information Science9

Health Care6

Concomitant activation of pathways downstream of Grb2 and PI 3-kinase is required for MET-mediated metastasis. (1/4818)

ATF-2-binding regulatory element is responsible for the Ly49A expression in murine T lymphoid line, EL-4. (2/4818)

Identification of a cAMP response element within the glucose- 6-phosphatase hydrolytic subunit gene promoter which is involved in the transcriptional regulation by cAMP and glucocorticoids in H4IIE hepatoma cells. (3/4818)

Analysis of 4-phosphopantetheinylation of polyhydroxybutyrate synthase from Ralstonia eutropha: generation of beta-alanine auxotrophic Tn5 mutants and cloning of the panD gene region. (4/4818)

An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. (5/4818)

Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. (6/4818)

A binding site for homeodomain and Pax proteins is necessary for L1 cell adhesion molecule gene expression by Pax-6 and bone morphogenetic proteins. (7/4818)

Functional analysis of the promoter of the yeast SNQ2 gene encoding a multidrug resistance transporter that confers the resistance to 4-nitroquinoline N-oxide. (8/4818)

No FAQ available that match "consensus sequence"

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Consensus Sequence

Molecular Sequence Data

Base Sequence

Consensus

Amino Acid Sequence

Promoter Regions, Genetic

Binding Sites

Cloning, Molecular

Transcription, Genetic

Sequence Homology, Nucleic Acid

Sequence Alignment

DNA

Sequence Homology, Amino Acid

DNA-Binding Proteins

Transcription Factors

Consensus Development Conferences as Topic

Sequence Analysis, DNA

Plasmids

Escherichia coli

Protein Binding

Restriction Mapping

Regulatory Sequences, Nucleic Acid

Mutagenesis, Site-Directed

Mutation

Introns

Repetitive Sequences, Nucleic Acid

RNA, Messenger

Interferon Regulatory Factors

Cell Line

DNA Primers

Genes, Bacterial

Bacterial Proteins

Genes

Gene Expression Regulation

DNA, Complementary

Polymerase Chain Reaction

DNA, Bacterial

Recombinant Fusion Proteins

Recombinant Proteins

Repressor Proteins

Conserved Sequence

Transfection

Exons

Oligodeoxyribonucleotides

RNA Splicing

Nucleic Acid Conformation

Gene Expression Regulation, Bacterial

Operon

Amino Acid Motifs

Electrophoretic Mobility Shift Assay

Protein Structure, Tertiary

Enhancer Elements, Genetic

Substrate Specificity

Phylogeny

Saccharomyces cerevisiae

DNA, Fungal

Sequence Deletion

Gene Library

Nuclear Proteins

Genes, Regulator

Chloramphenicol O-Acetyltransferase

Delphi Technique

Sequence Analysis

Chromosome Mapping

HeLa Cells

DNA Restriction Enzymes

Models, Molecular

Response Elements

DNA Footprinting

Oligonucleotide Probes

DNA Mutational Analysis

Deoxyribonuclease I

Phosphorylation

Open Reading Frames

Trans-Activators

Zinc Fingers

Peptides

Carrier Proteins

Glycosylation

DNA Transposable Elements