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).
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.
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.
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 degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The functional hereditary units of BACTERIA.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
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.
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 functional hereditary units of VIRUSES.
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.
Proteins found in any species of virus.
Proteins found in any species of bacterium.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
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.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
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).
The relationships of groups of organisms as reflected by their genetic makeup.
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)
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.
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.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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.
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.
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.
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.
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.
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.
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 method used for determining the location of and relative distances between genes on a chromosome.
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.
Ribonucleic acid that makes up the genetic material of viruses.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
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 three possible sequences of CODONS by which GENETIC TRANSLATION may occur from one nucleotide sequence. A segment of mRNA 5'AUCCGA3' could be translated as 5'AUC.. or 5'UCC.. or 5'CCG.., depending on the location of the START CODON.
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 phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Proteins prepared by recombinant DNA technology.
Established cell cultures that have the potential to propagate indefinitely.
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).
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.
The functional hereditary units of FUNGI.
Viral proteins that are components of the mature assembled VIRUS PARTICLES. They may include nucleocapsid core proteins (gag proteins), enzymes packaged within the virus particle (pol proteins), and membrane components (env proteins). These do not include the proteins encoded in the VIRAL GENOME that are produced in infected cells but which are not packaged in the mature virus particle,i.e. the so called non-structural proteins (VIRAL NONSTRUCTURAL PROTEINS).
A codon that directs initiation of protein translation (TRANSLATION, GENETIC) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon.
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.
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.
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 sum of the weight of all the atoms in a molecule.
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.
Viruses parasitic on plants higher than bacteria.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
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.
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).
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.
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.
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.
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)
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.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
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.
The type species of VARICELLOVIRUS causing CHICKENPOX (varicella) and HERPES ZOSTER (shingles) in humans.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The genetic complement of a BACTERIA as represented in its DNA.
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.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
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.
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 spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
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.
A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.
Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
Proteins obtained from ESCHERICHIA COLI.
Proteins found in any species of fungus.
A genus of bacteria that form a nonfragmented aerial mycelium. Many species have been identified with some being pathogenic. This genus is responsible for producing a majority of the ANTI-BACTERIAL AGENTS of practical value.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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.
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)
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Viruses whose genetic material is RNA.
A directed change in translational READING FRAMES that allows the production of a single protein from two or more OVERLAPPING GENES. The process is programmed by the nucleotide sequence of the MRNA and is sometimes also affected by the secondary or tertiary mRNA structure. It has been described mainly in VIRUSES (especially RETROVIRUSES); RETROTRANSPOSONS; and bacterial insertion elements but also in some cellular genes.
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.
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.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Transport proteins that carry specific substances in the blood or across cell membranes.
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.
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.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
The sequential location of genes on a chromosome.
A cognitive disorder characterized by an impaired ability to comprehend written and printed words or phrases despite intact vision. This condition may be developmental or acquired. Developmental dyslexia is marked by reading achievement that falls substantially below that expected given the individual's chronological age, measured intelligence, and age-appropriate education. The disturbance in reading significantly interferes with academic achievement or with activities of daily living that require reading skills. (From DSM-IV)
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.
The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.
A species of gram-positive bacteria that is a common soil and water saprophyte.
A CELL LINE derived from the kidney of the African green (vervet) monkey, (CERCOPITHECUS AETHIOPS) used primarily in virus replication studies and plaque assays.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Layers of protein which surround the capsid in animal viruses with tubular nucleocapsids. The envelope consists of an inner layer of lipids and virus specified proteins also called membrane or matrix proteins. The outer layer consists of one or more types of morphological subunits called peplomers which project from the viral envelope; this layer always consists of glycoproteins.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Viruses which produce a mottled appearance of the leaves of plants.
A species in the genus RHADINOVIRUS, subfamily GAMMAHERPESVIRINAE, isolated from patients with AIDS-related and "classical" Kaposi sarcoma.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
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.
Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.
A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Viruses whose hosts are bacterial cells.
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 family of small, non-enveloped DNA viruses infecting birds and most mammals, especially humans. They are grouped into multiple genera, but the viruses are highly host-species specific and tissue-restricted. They are commonly divided into hundreds of papillomavirus "types", each with specific gene function and gene control regions, despite sequence homology. Human papillomaviruses are found in the genera ALPHAPAPILLOMAVIRUS; BETAPAPILLOMAVIRUS; GAMMAPAPILLOMAVIRUS; and MUPAPILLOMAVIRUS.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.
A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.
The type species of ORTHOPOXVIRUS, related to COWPOX VIRUS, but whose true origin is unknown. It has been used as a live vaccine against SMALLPOX. It is also used as a vector for inserting foreign DNA into animals. Rabbitpox virus is a subspecies of VACCINIA VIRUS.
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.
The rate dynamics in chemical or physical systems.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
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.
The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
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.
Genotypic differences observed among individuals in a population.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
Nucleic acid sequences involved in regulating the expression of genes.
Viruses infecting insects, the largest family being BACULOVIRIDAE.
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.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
A positive-stranded RNA virus species in the genus HEPEVIRUS, causing enterically-transmitted non-A, non-B hepatitis (HEPATITIS E).
A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.
A process of GENETIC TRANSLATION whereby the formation of a peptide chain is started. It includes assembly of the RIBOSOME components, the MESSENGER RNA coding for the polypeptide to be made, INITIATOR TRNA, and PEPTIDE INITIATION FACTORS; and placement of the first amino acid in the peptide chain. The details and components of this process are unique for prokaryotic protein biosynthesis and eukaryotic protein biosynthesis.
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.
Family of INSECT VIRUSES containing two subfamilies: Eubaculovirinae (occluded baculoviruses) and Nudibaculovirinae (nonoccluded baculoviruses). The Eubaculovirinae, which contain polyhedron-shaped inclusion bodies, have two genera: NUCLEOPOLYHEDROVIRUS and GRANULOVIRUS. Baculovirus vectors are used for expression of foreign genes in insects.
Proteins that are coded by immediate-early genes, in the absence of de novo protein synthesis. The term was originally used exclusively for viral regulatory proteins that were synthesized just after viral integration into the host cell. It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals.
Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Biochemical identification of mutational changes in a nucleotide sequence.
A genus of the family HERPESVIRIDAE, subfamily BETAHERPESVIRINAE, infecting the salivary glands, liver, spleen, lungs, eyes, and other organs, in which they produce characteristically enlarged cells with intranuclear inclusions. Infection with Cytomegalovirus is also seen as an opportunistic infection in AIDS.
Enzymes that recombine DNA segments by a process which involves the formation of a synapse between two DNA helices, the cleavage of single strands from each DNA helix and the ligation of a DNA strand from one DNA helix to the other. The resulting DNA structure is called a Holliday junction which can be resolved by DNA REPLICATION or by HOLLIDAY JUNCTION RESOLVASES.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Any codon that signals the termination of genetic translation (TRANSLATION, GENETIC). PEPTIDE TERMINATION FACTORS bind to the stop codon and trigger the hydrolysis of the aminoacyl bond connecting the completed polypeptide to the tRNA. Terminator codons do not specify amino acids.
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.
One of the Type II site-specific deoxyribonucleases (EC It recognizes and cleaves the sequence A/AGCTT at the slash. HindIII is from Haemophilus influenzae R(d). Numerous isoschizomers have been identified. EC 3.1.21.-.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
Insects of the suborder Heterocera of the order LEPIDOPTERA.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Proteins that form the CAPSID of VIRUSES.
A non-pathogenic species of LACTOCOCCUS found in DAIRY PRODUCTS and responsible for the souring of MILK and the production of LACTIC ACID.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
A genus of the family BACULOVIRIDAE, subfamily Eubaculovirinae, characterized by the formation of crystalline, polyhedral occlusion bodies in the host cell nucleus. The type species is Autographa californica nucleopolyhedrovirus.
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 species of DELTAPAPILLOMAVIRUS infecting cattle.
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.
Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.
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).
Proteins transcribed from the E4 region of ADENOVIRUSES. The E4 19K protein transactivates transcription of the adenovirus E2F protein and complexes with it.
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.
Diseases of plants.
Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.
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 functional hereditary units of PLANTS.
A parasexual process in BACTERIA; ALGAE; FUNGI; and ciliate EUKARYOTA for achieving exchange of chromosome material during fusion of two cells. In bacteria, this is a uni-directional transfer of genetic material; in protozoa it is a bi-directional exchange. In algae and fungi, it is a form of sexual reproduction, with the union of male and female gametes.
A genus of PARVOVIRIDAE, subfamily DENSOVIRINAE, comprising helper-independent viruses containing only two species. Junonia coenia densovirus is the type species.
The heritable modification of the properties of a competent bacterium by naked DNA from another source. The uptake of naked DNA is a naturally occuring phenomenon in some bacteria. It is often used as a GENE TRANSFER TECHNIQUE.
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.
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.
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 a DNA molecule is duplicated.
The type species of RHADINOVIRUS, in the subfamily GAMMAHERPESVIRINAE, isolated from squirrel monkeys. It produces malignant lymphomas (LYMPHOMA, MALIGNANT) in inoculated marmosets or owl monkeys.
A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by complex contractile tails.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
A subfamily of HERPESVIRIDAE characterized by variable reproductive cycles. The genera include: LYMPHOCRYPTOVIRUS and RHADINOVIRUS.
Substances elaborated by specific strains of bacteria that are lethal against other strains of the same or related species. They are protein or lipopolysaccharide-protein complexes used in taxonomy studies of bacteria.
Proteins from the family Retroviridae. The most frequently encountered member of this family is the Rous sarcoma virus protein.
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.
Products of viral oncogenes, most commonly retroviral oncogenes. They usually have transforming and often protein kinase activities.
Substances elaborated by viruses that have antigenic activity.
The complete gene complement contained in a set of chromosomes in a fungus.
A genus of PLANT VIRUSES, in the family CAULIMOVIRIDAE, that are transmitted by APHIDS in a semipersistent manner. Aphid-borne transmission of some caulimoviruses requires certain virus-coded proteins termed transmission factors.
A genus of gram-negative, aerobic, rod-shaped bacteria that activate PLANT ROOT NODULATION in leguminous plants. Members of this genus are nitrogen-fixing and common soil inhabitants.
A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.
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.
Actual loss of portion of a chromosome.
The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.
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.
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.
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.
A genus of owlet moths of the family Noctuidae. These insects are used in molecular biology studies during all stages of their life cycle.
DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.

In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron. (1/11650)

The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual twin-ribozyme organization. One of the ribozymes (DiGIR2) catalyses intron excision and exon ligation. The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open reading frame (ORF) is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1 and IPS2) located at its 3' end. Examination of the in vivo expression of DiSSU1 shows that after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed cleavage upstream of the ORF 5' end, as well as truncation and polyadenylation downstream of the ORF 3' end. A spliceosomal intron, the first to be reported within a group I intron and the rDNA, is removed before the I-DirI mRNA associates with the polysomes. Taken together, our results imply that DiSSU1 uses a unique combination of intron-supplied ribozyme activity and adaptation to the general RNA polymerase II pathway of mRNA expression to allow a protein to be produced from the RNA polymerase I-transcribed rDNA.  (+info)

A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (2/11650)

Premature translation termination codon (PTC)-mediated effects on nuclear RNA processing have been shown to be associated with a number of human genetic diseases; however, how these PTCs mediate such effects in the nucleus is unclear. A PTC at nucleotide (nt) 2018 that lies adjacent to the 5' element of a bipartite exon splicing enhancer within the NS2-specific exon of minute virus of mice P4 promoter-generated pre-mRNA caused a decrease in the accumulated levels of P4-generated R2 mRNA relative to P4-generated R1 mRNA, although the total accumulated levels of P4 product remained the same. This effect was seen in nuclear RNA and was independent of RNA stability. The 5' and 3' elements of the bipartite NS2-specific exon enhancer are redundant in function, and when the 2018 PTC was combined with a deletion of the 3' enhancer element, the exon was skipped in the majority of the viral P4-generated product. Such exon skipping in response to a PTC, but not a missense mutation at nt 2018, could be suppressed by frame shift mutations in either exon of NS2 which reopened the NS2 open reading frame, as well as by improvement of the upstream intron 3' splice site. These results suggest that a PTC can interfere with the function of an exon splicing enhancer in an open reading frame-dependent manner and that the PTC is recognized in the nucleus.  (+info)

Comparative sequence analysis of human minisatellites showing meiotic repeat instability. (3/11650)

The highly variable human minisatellites MS32 (D1S8), MS31A (D7S21), and CEB1 (D2S90) all show recombination-based repeat instability restricted to the germline. Mutation usually results in polar interallelic conversion or occasionally in crossovers, which, at MS32 at least, extend into DNA flanking the repeat array, defining a localized recombination hotspot and suggesting that cis-acting elements in flanking DNA can influence repeat instability. Therefore, comparative sequence analysis was performed to search for common flanking elements associated with these unstable loci. All three minisatellites are located in GC-rich DNA abundant in dispersed and tandem repetitive elements. There were no significant sequence similarities between different loci upstream of the unstable end of the repeat array. Only one of the three loci showed clear evidence for putative coding sequences near the minisatellite. No consistent patterns of thermal stability or DNA secondary structure were shared by DNA flanking these loci. This work extends previous data on the genomic environment of minisatellites. In addition, this work suggests that recombinational activity is not controlled by primary or secondary characteristics of the DNA sequence flanking the repeat array and is not obviously associated with gene promoters as seen in yeast.  (+info)

Kinetoplast DNA minicircles of Leishmania donovani express a protein product. (4/11650)

We describe an unprecedented finding of an open reading frame present in the variable region in one of the minicircle sequence classes of a human pathogenic strain of Leishmania donovani (MHOM/IN/90/RMRI 68) which is transcribed and translated. The encoded protein showed homologies to known transport proteins.  (+info)

Identification of a cytolethal distending toxin gene locus and features of a virulence-associated region in Actinobacillus actinomycetemcomitans. (5/11650)

A genetic locus for a cytolethal distending toxin (CDT) was identified in a polymorphic region of the chromosome of Actinobacillus actinomycetemcomitans, a predominant oral pathogen. The locus was comprised of three open reading frames (ORFs) that had significant amino acid sequence similarity and more than 90% sequence identity to the cdtABC genes of some pathogenic Escherichia coli strains and Haemophilus ducreyi, respectively. Sonic extracts from recombinant E. coli, containing the A. actinomycetemcomitans ORFs, caused the distension and killing of Chinese hamster ovary cells characteristic of a CDT. Monoclonal antibodies made reactive with the CdtA, CdtB, and CdtC proteins of H. ducreyi recognized the corresponding gene products from the recombinant strain. CDT-like activities were no longer expressed by the recombinant strain when an OmegaKan-2 interposon was inserted into the cdtA and cdtB genes. Expression of the CDT-like activities in A. actinomycetemcomitans was strain specific. Naturally occurring expression-negative strains had large deletions within the region of the cdt locus. The cdtABC genes were flanked by an ORF (virulence plasmid protein), a partial ORF (integrase), and DNA sequences (bacteriophage integration site) characteristic of virulence-associated regions. These results provide evidence for a functional CDT in a human oral pathogen.  (+info)

Complete nucleotide sequence of the 27-kilobase virulence related locus (vrl) of Dichelobacter nodosus: evidence for extrachromosomal origin. (6/11650)

The vrl locus is preferentially associated with virulent isolates of the ovine footrot pathogen, Dichelobacter nodosus. The complete nucleotide sequence of this 27.1-kb region has now been determined. The data reveal that the locus has a G+C content much higher than the rest of the D. nodosus chromosome and contains 22 open reading frames (ORFs) encoding products including a putative adenine-specific methylase, two potential DEAH ATP-dependent helicases, and two products with sequence similarity to a bacteriophage resistance system. These ORFs are all in the same orientation, and most are either overlapping or separated by only a few nucleotides, suggesting that they comprise an operon and are translationally coupled. Expression vector studies have led to the identification of proteins that correspond to many of these ORFs. These data, in combination with evidence of insertion of vrl into the 3' end of an ssrA gene, are consistent with the hypothesis that the vrl locus was derived from the insertion of a bacteriophage or plasmid into the D. nodosus genome.  (+info)

Characterization of Moraxella (Branhamella) catarrhalis lbpB, lbpA, and lactoferrin receptor orf3 isogenic mutants. (7/11650)

Pathogenic members of the family Neisseriaceae produce specific receptors to acquire iron from their host's lactoferrin and transferrin. Recently, putative Moraxella catarrhalis lactoferrin receptor genes and a third open reading frame (lbpB, lbpA, and orf3) were cloned and sequenced. We describe the preliminary characterization of isogenic mutants deficient in LbpB, LbpA, or Orf3 protein.  (+info)

Cloning, molecular analysis and differential cell localisation of the p36 RACK analogue antigen from the parasite protozoon Crithidia fasciculata. (8/11650)

The family of the RACK molecules (receptors for activated C kinases) are present in all the species studied so far. In the genus Leishmania, these molecules also induce a strong immune reaction against the infection. We have cloned and characterised the gene that encodes the RACK analogue from the parasite trypanosomatid Crithidia fasciculata (CACK). The molecule seems to be encoded by two genes. The sequence analysis of the cloned open reading frame indicates the existence of a high degree of conservation not only with other members of the Trypanosomatidae but also with mammalians. The study of the protein kinase C phosphorylation sites shows the presence of three of them, shared with the mammalian species, additional to those present in the other protozoa suggesting a certain phylogenetic distance between the protozoon Crithidia fasciculata and the rest of the Trypanosomatidae. The CACK-encoded polypeptide shows an additional sequence of four amino acids at the carboxy-terminal end, which produces a different folding of the fragment with the presence of an alpha-helix instead of the beta-sheet usual in all the other species studied. A similar result is elicited at the amino-terminal end by the change of three amino acid residues. The immunolocalisation experiments show that the CACK displays a pattern with a distribution mainly at the plasma membrane, different from that of the related Leishmania species used as control, that displays a distribution close to the nucleus. Altogether, the data suggest that the existence of the structural differences found may have functional consequences.  (+info)

Read Rat cytomegalovirus open reading frame R44 is an early-late gene that encodes a nuclear protein, Archives of Virology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
TY - JOUR. T1 - Human papillomavirus (HPV) types 101 and 103 isolated from cervicovaginal cells lack an E6 open reading frame (ORF) and are related to gamma-papillomaviruses. AU - Chen, Zigui. AU - Schiffman, Mark. AU - Herrero, Rolando. AU - DeSalle, Rob. AU - Burk, Robert D.. PY - 2007/4/10. Y1 - 2007/4/10. N2 - Complete genomes of HPV101 and HPV103 were PCR amplified and cloned from cervicovaginal cells of a 34-year-old female with cervical intraepithelial neoplasia grade 3 (CIN 3) and a 30-year-old female with a normal Pap test, respectively. HPV101 and HPV103 contain 4 early genes (E7, E1, E2, and E4) and 2 late genes (L2 and L1), but both lack the canonical E6 ORF. Pairwise alignment similarity of the L1 ORF nucleotide sequences of HPV101 and HPV103 indicated that they are at least 30% dissimilar to each other and all known PVs. However, similarities of the other ORFs (E7, E1, E2, and L2) indicated that HPV101 and HPV103 are most related to each other. Phylogenetic analyses revealed that ...
TY - JOUR. T1 - Identification of a novel 23 kDa protein encoded by putative open reading frame 2 of TT virus (TTV) genotype 1 different from the other genotypes. AU - Tanaka, Y.. AU - Orito, E.. AU - Ohno, T.. AU - Nakano, T.. AU - Hayashi, K.. AU - Kato, T.. AU - Mukaide, M.. AU - Iida, S.. AU - Mizokami, M.. PY - 2000/1/1. Y1 - 2000/1/1. N2 - We report the entire open reading frames (ORFs) sequences of four TT virus (TTV) isolates, one genotype 2 (G2) and three G4 isolates. Despite a DNA virus, TTV possesses high rate of amino acid (aa) substitution: the aa sequence homology of ORF1 and 2 is lower than the nucleotide homology. The partial N22 region of ORF1 is suitable for genotyping of prototype TTV isolates, because the phylogenetic tree from partial N22 sequence is consistent with that from the entire ORF1. Based on our sequence data, ORF2 from most isolates excluding G1 encode truncated 49 aa (pORF2a) because of an in-frame stop codon, although ORF2s from most G1 isolates encode 202 ...
Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants. We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs. This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (|150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved
TY - JOUR. T1 - Genes within genes. T2 - independent expression of phage T4 intron open reading frames and the genes in which they reside.. AU - Gott, J. M.. AU - Zeeh, A.. AU - Bell-Pedersen, D.. AU - Ehrenman, Karen. AU - Belfort, M.. AU - Shub, D. A.. PY - 1988/1/1. Y1 - 1988/1/1. N2 - The td, nrdB, and sunY introns of bacteriophage T4 each contain a long open reading frame (ORF). These ORFs are preceded by functional T4 late promoters and, in the case of the nrdB intron ORF, a functional middle promoter. Expression of phage-encoded intron ORF-lacZ fusions indicates that these T4 genes are highly regulated. The lack of translation of these ORFs from early pre-mRNAs can be accounted for by the presence of secondary structures that are absent from the late RNAs. Because translation of the intron ORFs could disrupt core structural elements required for pre-mRNA splicing, such regulation may be necessary to allow expression of the genes in which they reside.. AB - The td, nrdB, and sunY introns ...
Background Within the scanning model of translation initiation, reinitiation is a non-canonical mechanism that operates on mRNAs harboring upstream open reading frames. The h subunit of eukaryotic initiation factor 3 (eIF3) boosts translation reinitiation on the uORF-containing mRNA coding for the Arabidopsis bZip transcription factor, AtbZip11, among others. The RPL24B protein of the large ribosomal subunit, which is encoded by SHORT VALVE1, likewise fosters translation of uORF-containing mRNAs, for example mRNAs for auxin response transcription factors (ARFs). Results Here we tested the hypothesis that RPL24B and eIF3h affect translation reinitiation in a similar fashion. First, like eif3h mutants, rpl24b mutants under-translate the AtbZip11 mRNA, and the detailed spectrum of translational defects in rpl24b is remarkably similar to that of eif3h. Second, eif3h mutants display defects in auxin mediated organogenesis and gene expression, similar to rpl24b. Like AtbZip11, the uORF-containing ARF mRNAs
TY - JOUR. T1 - Conservation of the influenza virus membrane protein (M1) amino acid sequence and an open reading frame of RNA segment 7 encoding a second protein (M2) in H1N1 and H3N2 strains. AU - Lamb, Robert A.. AU - Lai, Ching Juh. PY - 1981/7/30. Y1 - 1981/7/30. N2 - The complete sequence of a full-length cloned DNA copy of the influenza virus A/Udorn/72 (H3N2) RNA segment 7 has been determined. A second open reading frame has been found which overlaps the membrane protein (M1) sequence by 68 nucleotides. This second reading frame could code, in the +1 reading frame, for a protein (M2) with a maximum of 97 amino acids depending on whether there is splicing of the mRNA and the methionine residue used for initiation of protein synthesis. Comparison of the present H3N2 sequence with the previously published sequence (G. Winter and S. Fields, Nucleic Acids Res., 8, 1965-1975, 1980; H. Allen, J. McCauley, M. Waterfield, and M.-J. Gething, Virology, 107, 548-551, 1980) of RNA segment 7 of ...
Theres a great guide regarding how to ensure that the automated gene annotator that identified the gene youre working on chose the proper start location for translation. The guide is in Dropbox (you dont need an account in Dropbox to get these, but its handy free cloud storage.) The guide can be downloaded here ...
Flannick J, Thorleifsson G, Beer NL, Jacobs SB, Grarup N, Burtt NP, Mahajan A, Fuchsberger C, Atzmon G, Benediktsson R, Blangero J, Bowden DW, Brandslund I, Brosnan J, Burslem F, Chambers J, Cho YS, Christensen C, Douglas DA, Duggirala R, Dymek Z, Farjoun Y, Fennell T, Fontanillas P, Forsén T, Gabriel S, Glaser B, Gudbjartsson DF, Hanis C, Hansen T, Hreidarsson AB, Hveem K, Ingelsson E, Isomaa B, Johansson S, Jørgensen T, Jørgensen ME, Kathiresan S, Kong A, Kooner J, Kravic J, Laakso M, Lee JY, Lind L, Lindgren CM, Linneberg A, Masson G, Meitinger T, Mohlke KL, Molven A, Morris AP, Potluri S, Rauramaa R, Ribel-Madsen R, Richard AM, Rolph T, Salomaa V, Segrè AV, Skärstrand H, Steinthorsdottir V, Stringham HM, Sulem P, Tai ES, Teo YY, Teslovich T, Thorsteinsdottir U, Trimmer JK, Tuomi T, Tuomilehto J, Vaziri-Sani F, Voight BF, Wilson JG, Boehnke M, McCarthy MI, Njølstad PR, Pedersen O, Groop L, Cox DR, Stefansson K, Altshuler D. Loss-of-function mutations in SLC30A8 protect against type 2 ...
Research groupsGene regulation and morphogenesis Genetics and functional genomics of genes with small open reading frames Dr Juan Pablo ..
Research groupsGene regulation and morphogenesis Genetics and functional genomics of genes with small open reading frames Dr Juan Pablo ..
Genome map of SSV1. Open reading frames are shown as block arrows and labeled as in Palm et al. (1991). Virus structural protein genes (Reiter et al., 1987a) an
Virions are constructed from a major capsid protein (CP) encoded by the second open reading frame (ORF2). The CP binds to surface heparin sulfate proteoglycans (HSPGs) on liver cells (Kalia et al., 2009) and may be proteolytically processed. A small immunoreactive protein (113-114 amino acids, 12.5 kDa) encoded by the third ORF (ORF3) has been identified and shown to exhibit multiple functions associated with virion morphogenesis, egress and viral pathogenesis. Recently, the ORF3 polypeptide has been shown to share several structural features with class I viroporins (Ding et al., 2017). Non-structural proteins encoded by the first major ORF (ORF1) have limited similarity with the alpha-like supergroup of viruses and contain domains consistent with a methyltransferase, papain-like cysteine protease, macro domain, RNA helicase and RNA-dependent RNA polymerase (Cao and Meng 2012). Some of these predicted enzymatic properties have been confirmed experimentally (Karpe and Lole 2010, Parvez 2015, ...
Upstream open reading frames (uORFs) are small open reading frames found in the 5 UTR of a mature mRNA, and can potentially mediate translational regulation of the largest, or major, ORF (mORF). CPuORF30 represents a conserved upstream opening reading frame relative to major ORF AT3G18000.1 ...
Codons consist of six bases and there are six reading frames for each DNA strand, so ... so researchers must evaluate six open reading frames.
(KudoZ) English to Polish translation of complete open reading frame of a cDNA molecule: otwarta ramka odczytu (cząsteczki cDNA) [Medical].
Stern-Ginossar and the other researchers suspected that existing maps of HCMVs protein-coding potential, based largely on computational methods, were far from complete. So, they began mapping the positions of ribosomes-the cellular organelles in which proteins are synthesized-during an HCMV infection of human fibroblast cells. With the resulting map, Stern-Ginossar and her colleagues discovered templates for hundreds of previously unidentified proteins that were encoded in corresponding DNA segments of the viral genome, known as open reading frames.. Surprisingly, the researchers found that many of these open reading frames encode for exceptionally short protein sequences (fewer than 100 amino acids). And some of the newly identified open reading frames were even hiding inside other open reading frames, they say.. A key finding of our work is that each of these templates can encode more than one protein, said Annette Michalski from the Max Planck Institute of Biochemistry in Martinsried, ...
Myc-DDK-tagged ORF clone of Homo sapiens chromosome 5 open reading frame 13 (C5orf13), transcript variant 3 as transfection-ready DNA - 10 µg - OriGene - cdna clones
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and
Myc-DDK-tagged ORF clone of Homo sapiens chromosome 10 open reading frame 122 (C10orf122) as transfection-ready DNA - 10 µg - OriGene - cdna clones
TY - JOUR. T1 - Yeast CAL1 is a structural and functional homologue to the DPR1 (RAM) gene involved in ras processing. AU - Ohya, Yoshikazu. AU - Goebl, Mark. AU - Goodman, Laurie E.. AU - Petersen-Bjørn, Sara. AU - Friesen, James D.. AU - Tamanoi, Fuyuhiko. AU - Anraku, Yasuhiro. PY - 1991. Y1 - 1991. N2 - A 2.3-kilobase pair DNA fragment of the yeast CAL1 gene was cloned by complementation of the cal1-1 mutation, which causes a defect in nuclear division and bud formation (Ohya, Y., Ohsumi, Y., and Anraku, Y. (1984) Mol. & Gen. Genet. 193, 389-394). Nucleotide sequencing of this fragment revealed a single open reading frame (ORF) encoding a polypeptide of 376 amino acids. Comparative analysis of the predicted amino acid sequence has shown that the CAL1 product has similarity to two yeast proteins: the DPR1 (RAM) gene product that is involved in processing of ras protein at the farnesylation step, and the essential ORF2 protein whose structural gene has a head-to-head arrangement with PRP4, ...
The BY4741 strain used in (Nagalakshmi et al. 2008) was used in this study. RNA-Seq was performed using the protocol developed in (Nagalakshmi et al. 2008), further described in (Nagalakshmi et al. 2010) and (Waern et al. 2011), and using the modifications developed by (Parkhomchuk et al. 2009) to generate strand-specific reads.. Analysis was performed on custom software developed in-house using BowTie (Langmead et al. 2009) to map reads to the S288C reference genome available on SGD, downloaded on May 17, 2010. Python, NumPy, SciPy, and matplotlib were used to further process the data. The softwares source code is available (Saccharomyces Genome Database). Of note, to maximize the information gleaned, unmappable reads were trimmed by four bases from the 3′ end and remapping was attempted; this was done iteratively until only 28 bp remained, at which point the read was considered unmappable. This end trimming typically doubled or more the number of mappable reads.. Expression levels were ...
Sorts alternative splicing (AS) and discovers coding potential. spliceR simplifies downstream sequence analysis by allowing annotation of genomic coordinates of the differentially spliced elements. It is able to detect coding potential of transcripts, determines untranslated region (UTR) and open reading frame (ORF) lengths and predicts whether transcripts are nonsense mediated decay (NMD)-sensitive based on compatible annotated start codon positions and their downstream ORF.
C20orf203 is a de novo human gene that evolved from non-coding DNA after the split between human and chimp. In the human lineage 5 point mutations in the region resulted in the creation of an open reading frame which lead to the expression and translation of 194 amino acid (22kDa) protein. This protein is enriched in the brain and is up regulated in the brains of Alzheimers patients and thus has been hypothesized to play a role in the pathogenesis of this disease.. ...
Abstract: Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ambigrammatic and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be ...
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The structures of both eukaryotic and prokaryotic genes involve several nested sequence elements. Each element has a specific function in the multi-step process of gene expression. The sequences and lengths of these elements vary, but the same general functions are present in most genes.[2] Although DNA is a double-stranded molecule, typically only one of the strands encodes information that the RNA polymerase reads to produce protein-coding mRNA or non-coding RNA. This sense or coding strand, runs in the 5 to 3 direction where the numbers refer to the carbon atoms of the backbones ribose sugar. The open reading frame (ORF) of a gene is therefore usually represented as an arrow indicating the direction in which the sense strand is read.[10] Regulatory sequences are located at the extremities of genes. These sequence regions can be next to the transcribed region (the promoter) or separated by many kilobases (enhancers and silencers).[11] The promoter is located at the 5 end of the gene ...
Briefly explain the following terms gene expression point mutation BLAST transgenic organism Open reading frame Restriction endonuclease Regulation of gene ...
Predicting open reading frames within genomic sequences is probably one of the most basic yet important hallmarks of bioinformatics and sequencing analysis. This is the process by which, given an organisms genomic sequence or a section of that genomic sequence, we predict what sections of that genome are potential genes. At its most basic level, this can be done by looking for sequence regions between start and stop codons (sequence signals for the beginning and end of a gene). While there are many programs for predicting open reading frames, I often use the common Glimmer3 toolkit. This program works great overall, but one drawback is that it can sometimes be hard to visualize your open reading frames on your genome or genomic region (using Geneious or the Integrated Genomics Viewer) because it does not give you a .gff3 formatted file, which is commonly used by these programs. In this technical post, I am going to focus on the file types you get from Glimmer3, I will explain the .gff3 file ...
LOC101241902 (chromosome 4 open reading frame 46 pseudogene), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
Compare chromosome 9 open reading frame 62 Biomolecules from leading suppliers on Biocompare. View specifications, prices, citations, reviews, and more.
These plasmids were used in Phoebe Lus paper: Lu PD, Harding HP and Ron D. 2004. Translation re-initiation at alternative open reading frames regulates gene expression in an integrated stress response. J Cell Biol. 167:27-33.. Important Note: These ...
p,Transcripts that dont contain an open reading frame (ORF) and cannot be placed in one of the other categories.,/p,Processed transcript ...
from Bio import SeqIO ,,,record = SeqIO.read(sequence.fasta, fasta) ,,, table = 1 ,,, min_pro_len = 100 ,,,for strand, nuc in [(+1, record.seq), (-1, record.seq.reverse_complement())]: for frame in range(3): length = 3 * ((len(record)-frame) // 3) #Multiple of three for pro in nuc[frame:frame+length].translate(table).split(*): if len(pro) ,= min_pro_len: print(%s...%s - length %i, strand %i, frame %i \ % (pro[:30], pro[-3:], len(pro), strand, frame)) YSDIDQINLNQISNLQRNLKYFITMGDSTG...NNV - length 554, strand 1, frame 2 SSPGDKGHNCKGGSASSLCPHREEHHSHNG...ILT - length 162, strand -1, frame 1 IEHQDSHDDVQPTGYKEGDPPGREGCGTAA...HNW - length 216, strand -1, frame 1 TKVTGNVQATIITPIHVSPCSVVKCEVEKK...SDA - length 122, strand -1, frame 2 ...
We have taken a first step towards learning which upstream Open Reading Frames (uORFs) regulate gene expression (i.e., which uORFs are functional) in the yeast Saccharomyces cerevisiae. We do this by integrating data from several resources and combining a bioinformatics tool, ORF Finder, with a machine learning technique, inductive logic programming (ILP). Here, we report the challenge of using ILP as part of this integrative system, in order to automatically generate a model that identifies functional uORFs. Our method makes searching for novel functional uORFs more efficient than random sampling. An attempt has been made to predict novel functional uORFs using our method. Some preliminary evidence that our model may be biologically meaningful is presented.
Current Research: 1. Angiotensin receptor signaling and trafficking: The angiotensin type 1 receptor is a peptide hormone G protein-coupled receptor that is widely targeted to treat hypertension. We previously discovered that RNA binding proteins regulate the function of the rat type 1a receptor (AT1aR) by selectively binding within exon 2 of the receptor 5′-leader sequence and that this translational regulation is mediated by a short open reading frame in exon 2. More recently, this research direction has led to the exciting discovery of a seven amino acid peptide (PEP7) encoded within a short open reading frame in exon 2, which is a selective inhibitor of AT1aR signaling; PEP7 inhibits the Erk1/2 but not the classic inositol trisphosphate pathway. PEP7 may also contribute to age-related impairments in urine-concentrating mechanisms and modulates AT1aR trafficking. We study AT1aR signal transduction by conducting enzyme and radioligand binding assays as well as by measuring signaling ...
Upstream open reading frames (uORFs) are open reading frames that occur within the 5′ UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes.... Read more ...
Upstream open reading frames (uORFs) are open reading frames that occur within the 5′ UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes.... Read more ...
Abnova Human EXT1 Full-length ORF (NP_000118.2, 1 a.a. - 746 a.a.) Recombinant Protein with GST-tag at N-terminal 2µg Life Sciences:Protein Biology:Proteins:Proteins
Abnova Human ERAS Full-length ORF (NP_853510.1, 1 a.a. - 233 a.a.) Recombinant Protein with GST-tag at N-terminal 25µg Life Sciences:Protein Biology:Proteins:Proteins
We show that cytotoxic T lymphocytes (CTLs) infiltrating a kidney tumor recognize a peptide encoded by an alternative open reading frame (ORF) of the macrophage colony-stimulating factor (M-CSF) gene. Remarkably, this alternative ORF, which is translated in many tumors concurrently with the major ORF, is also translated in some tissues that do not produce M-CSF, such as liver and kidney. Such a dissociation of the translation of two overlapping ORFs from the same gene is unexpected. The antigenic peptide encoded by the alternative ORF is presented by human histocompatibility leukocyte antigen (HLA)-B*3501 and has a length of 14 residues. Peptide elution indicated that tumor cells naturally present this 14 mer, which is the longest peptide known to be recognized by CTLs. Binding studies of peptide analogues suggest that it binds by its two extremities and bulges out of the HLA groove to compensate for its length.
Translation of the polycistronic 35S RNA of CaMV (cauliflower mosaic virus) occurs via a reinitiation mechanism, which requires TAV (transactivator/viroplasmin). To allow translation reinitiation of the major open reading frames on the polycistronic RNA, TAV interacts with the host translational machinery via eIF3 (eukaryotic initiation factor 3) and the 60S ribosome. Accumulation of TAV and eIF3 in the polysomal fraction isolated from CaMV-infected cells suggested that TAV prevents loss of eIF3 from the translating ribosomes during the first initiation event. The TAV-eIF3-80S complex could be detected in vitro by sucrose-gradient-sedimentation analysis. The question is whether TAV interacts directly with the 48S preinitiation complex or enters polysomes after the first initiation event. eIF4B, a component of the 48S initiation complex, can preclude formation of the TAV-eIF3 complex via competition with TAV for eIF3 binding; the eIF4B- and TAV-binding sites on eIF3g overlap. eIF4B out-competes ...
TY - JOUR. T1 - Cloning and expression of Xenopus laevis xSox12 cDNA. AU - Komatsu, Naoki. AU - Hiraoka, Yoshiki. AU - Shiozawa, Masahide. AU - Ogawa, Motoyuki. AU - Aiso, Sadakazu. PY - 1996/3/1. Y1 - 1996/3/1. N2 - A family of SRY-related genes has been termed SOX. We have isolated and sequenced a cDNA encoding xSox12 from Xenopus laevis ovary. The cDNA contained an open reading frame (ORF) coding for 470 amino acids encompassing an HMG box characteristic of the SOX family, a leucine zipper motif and glutamine-rich segments. The size of the xSox12 mRNA was determined to be 3.0 knt by Northern analysis. The ovary was the most prominent in the expression of the Sox mRNA among the various tissues of adult frog as far as examined.. AB - A family of SRY-related genes has been termed SOX. We have isolated and sequenced a cDNA encoding xSox12 from Xenopus laevis ovary. The cDNA contained an open reading frame (ORF) coding for 470 amino acids encompassing an HMG box characteristic of the SOX family, a ...
TY - JOUR. T1 - Inactivation of the open reading frame slr0399 in Synechocystis sp. PCC 6803 functionally complements mutations near the Q(A) niche of photosystem II. A possible role of Slr0399 as a chaperone for quinone binding. AU - Ermakova-Gerdes, Svetlana. AU - Vermaas, Willem. PY - 1999/10/22. Y1 - 1999/10/22. N2 - The Synechocystis sp. PCC 6803 triple mutant D2R8 with V247M/A249T/M329I mutations in the D2 subunit of the photosystem II is impaired in Q(A) function, has an apparently mobile Q(A), and is unable to grow photoautotrophically. Several photoautotrophic pseudorevertants of this mutant have been isolated, each of which retained the original psbDI mutations of D2R8. Using a newly developed mapping technique, the site of the secondary mutations has been located in the open reading frame slr0399. Two different nucleotide substitutions and a deletion of about 60% of slr0399 were each shown to restore photoautotrophy in different pseudorevertants of the mutant D2R8, suggesting that ...
A human cytomegalovirus early gene which possesses three temporally regulated promoters is located in the large unique component of the viral genome between 0.054 and 0.064 map units (C.-P. Chang, C.L. Malone, and M.F. Stinski, J. Virol. 63:281-290, 1989). This gene contains a major open reading frame (ORF) located 233 bases downstream of the cap site of an early unspliced RNA. The major ORF predicts a polypeptide of 17 kilodaltons (kDa) which contains a glycoproteinlike signal and anchor domains as well as potential N-glycosylation sites. Antisera were prepared against synthetic peptides derived from amino acid sequences within the major ORF. The antisera detected a viral glycoprotein of 48 kDa in infected cells and recognized the in vitro-translated 17-kDa protein early-gene product. The viral glycoprotein, designated gp48, was modified by N-linked glycans and possibly O-linked glycans. The synthesis of gp48 occurred in the absence of viral DNA replication but accumulated to the highest levels ...
It has been shown previously, by sequence analysis of the S RNA segment of snowshoe hare (SSH) bunyavirus, that two overlapping open reading frames in the viral complementary sequence code for proteins with molecular weights of 26.8 X 10(3) and 10.5 X 10(3) respectively. In addition to the viral nucleocapsid (N) protein, which is coded by the S RNA, analyses of parental and reassortant bunyavirus-infected cell extracts have shown that the viral S RNA and M RNA species each code for non-structural proteins (NSS and NSM, respectively). In the present report, in vitro translation analyses of the S mRNA species recovered from virus-infected cells indicate that a single size class of mRNA directs the synthesis of N and NSS. Compositional analyses of selected tryptic peptides of N and NSS have provided proof that N is the product of the first open reading frame, and NSS the product of the second.
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Peanut yellow spot virus (PYSV) represents a distinct tospovirus species based on serology and nucleic acid hybridization. The sequence of the S RNA was 2 970 nucleotides with 22 nucleotide long inverted repeats (with three mismatches) at the termini. The coding was ambisense with a long open reading frame (ORF) in each strand. The 5-large ORF (1 440 nucleotides in the viral sense (v) strand) encoded a protein with a predicted size of 53.2 kDa that was identified as the nonstructural (NSs) protein based on 16-21% sequence identity and 42- 48% sequence similarity with other tospoviruses. A 3 ORF (741 nucleotides) in the virus complementary (vc) sense encoded a 28.0 kDa protein that was identified as the nucleocapsid (N) gene based on immuno-blot analysis of the in vitro expressed protein with PYSV polyclonal antiserum. The predicted N protein had 24-28% amino acid sequence identity and 44-51% sequence similarity with the members of other serogroups. In contrast to other tospoviruses, a third ORF (204
The combined sequences encoding a partial and putative rpsI open reading frame (ORF), non-coding (NC) region, a putative ORF for the Campylobacter adhesin to fibronectin-like protein (cadF), a putative Cla_0387 ORF, NC region and a partial and putative Cla_0388 ORF, were identified in 16 Campylobacter lari isolates, using two novel degenerate primer pairs. Probable consensus sequence at the -35 and -10 regions were identified in all C. lari isolates, as a promoter. Thus, cadF (-like) gene is highly conserved among C. lari organisms. Transcription of the cadF (-like) gene in C. lari cells in vivo was also confirmed and the transcription initiation site was determined. A peptidoglycan-associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins was completely conserved amongst the putative cadF (-like) ORFs from the C. lari isolates. The putative cadF (-like) ORFs from all C. lari isolates were nine amino acid larger than those from C. jejuni, and showed amino acid
TY - JOUR. T1 - First report of a novel alphapartitivirus in the basidiomycete Rhizoctonia oryzae-sativae. AU - Das, Subha. AU - Das, Sampa. PY - 2019/3/1. Y1 - 2019/3/1. N2 - Rhizoctonia oryzae-sativae is a soil-borne basidiomycete fungus that causes aggregate sheath spot disease on rice worldwide. Here, we report the complete genome sequence of a partitivirus designated as Rhizoctonia oryzae-sativae partitivirus 1 (RosPV1) infecting this fungus. The genome of RosPV1 consists of two double-stranded RNA (dsRNA) segments. The larger segment, designated as dsRNA-1 (1,961 bp), contains a single open reading frame (ORF) that encodes a putative polypeptide with a conserved RNA-dependent RNA polymerase (RdRp) domain. The smaller segment, dsRNA-2 (1,819 bp), also has a single ORF, which is predicted to encode the capsid protein (CP). BLAST searches and phylogenetic analyses suggested that RosPV1 is a representative member of a new species within the genus Alphapartitivirus. This is the first report of ...
Flowering time of rice (Oryza sativa L.) is among the most important agronomic traits for region adaptation and grain yield. In the process of rice breeding, efficient and slightly modulating the flowering time of an elite cultivar would be more popular with breeder. Hence, we are interested in slightly increasing the expression of flowering repressors by CRISPR/Cas9 genome editing system. It was predicated there were three uORFs in 5 leader sequence of Hd2. In this study, through editing Hd2 uORFs, we got four homozygous mutant lines. Phenotypic analysis showed that the hd2 urf edited lines flowered later by 4.6-11.2 days relative to wild type SJ2. Supporting the later flowering phenotype, the expression of Ehd1, Hd3a, and RFT1 is significantly decreased in hd2 urf than that in wild type. Moreover, we found that the transcription level of Hd2 is not affected, whereas the Hd2 protein level was increased in hd2 urf compared with wild type, which indicated that Hd2 uORFs indeed affect the translation of
We have previously described sigma A and sigma B and their structural genes, mysA and mysB, respectively, in Mycobacterium smegmatis. We have now sequenced the corresponding regions in the M. tuberculosis and M. leprae chromosomes, and have found the two homologous genes. The chromosomal linkage and the deduced amino acid (aa) sequences of the two genes show very high similarity in the three species of mycobacteria. We also report the finding of two other open reading frames (ORF) in these clusters. orfX, which has an unknown function, is located between mysA and mysB. The other ORF, located downstream from mysB, encodes a homolog of DtxR, the iron regulatory protein from Corynebacterium diphtheriae (Cd). Doukhan, L; Predich, M; Nair, G; Dussurget, O; Mandic-Mulec, I; Cole, S T; Smith, D R; Smith, I
The E4 region of human adenovirus type 2 is predicted to encode seven proteins as judged from its nucleotide sequence and the pattern of differential splicing of its transcript. Two of the open reading frames (ORFs), ORF1 and ORF2, had been identified as being disrupted in the recently published sequence of the related serotype 5 virus. These ORFs were resequenced and found to be intact in the wt300 strain of adenovirus type 5.
FusionGDB is the Fusion Gene annotation DataBase, aiming to provide a resource or reference for functional annotation of fusion genes in cancer for better therapeutic targets. We first collected 48 117 FGs across pan-cancer from three representative fusion gene resources: the improved database of chimeric transcripts and RNA-seq data (ChiTaRS 3.1), an integrative resource for cancer-associated transcript fusions (TumorFusions), and The Cancer Genome Atlas (TCGA) fusions by Gao et al. For these ~48K FGs, we performed functional annotations including gene assessment across pan-cancer fusion genes, open reading frame (ORF) assignment, and protein domain retention search based on multiple isoform gene structure with multiple break points and finally provided the fusion transcript and amino acid sequences for each break point and gene isoforms. For each fusion partner gene, the user can access multiple annotations such as gene summary, assessment scores of each gene in pan-cancer, biological process ...
In innate immune system, the response to invading pathogens is initiated by pattern recognition receptor (PRRs) that bind pathogen-associated molecular patterns (PAMPs) and arise various immune response. Lectins are well-knows PRRs that recognize the carbohydrate molecules on surface of pathogens. Galectins, known as S-type lectin, have a carbohydrate recognition domain (CRD), specificity for β-galactosides and Ca2+- independent activity. In this study, we described the molecular cloning and characterization of a cDNA sequence of galectin 3 from big belly seahorse, Hippocampus abdominalis. The HaGal3 cDNA includes an open reading frame (ORF) of 1068 bp with 5 untranslated region (UTR) of 83 bp and a 3 UTR of 214 bp. The ORF encoded a putative protein of 356 amino acids with a theoretical isoelectric point of 8.49 and predicted molecular mass of 38.6 kDa. The deduced protein includes a carbohydrate-recognition domain and a galactoside-type carbohydrate-binding motif H-NPR/W-E-R. HaGal3 showed ...
From the cloning and characterization of cDNAs, we found that the Epstein-Barr virus (EBV) open reading frame (ORF) BMLF1-BSLF2 coding for the early protein EB2 is present in several mRNAs generated by alternative splicing and expressed in the leftward direction from two promoters PM and PM1. The PM promoter controls the expression of two abundant mRNA species of 1.9 and 2 kilobases (kb), whereas the PM1 promoter controls the expression of at least three mRNAs 3.6, 4.0, and 4.4 kb long. The PM promoter probably overlaps with the PS promoter which controls the transcription of a 3.6-kb mRNA expressed in the rightward direction and containing the ORF BSRF1. Although it increases the amount of chloramphenicol acetyltransferase enzyme expressed from the chimeric pMCAT gene, EB2 is not a promiscuous trans-activator of gene expression and does not positively regulate its own expression from promoter PM. The EB2 activation is not promoter dependent but could possibly act by stabilizing mRNAs and ...
We expressed the M2 gene in prokaryotic cells using the pAED4 expression vector system to produce native and purified M2 protein as a candidate for universal recombinant vaccine against influenza A subtypes. The open reading frame (ORF) of avian influenza A/chicken/Iran/101/1998 (H9N2) M2 gene was amplified by 2-step RT-PCR using specific primers and pfu DNA polymerase. pAED4 was used as expression vector, purified PCR product digested by Nde I and EcoR I restriction enzymes was ligated to the same digested site in the vector using T4 ligase to form pAED4-M2. The cloned M2 gene was confirmed by PCR and restriction enzymes pattern. M2 polypeptide was produced through the expression of this recombinant expression vector (pAED4+M2) in Escherichia coli BL21 (DE3) strain. The expressed M2 polypeptide was analyzed on SDS-PAGE and confirmed by western blotting assay. The level of 100% homology between the N-terminal domain of H5 and H9 isolates was considerable. It seems that recombinant vaccine based ...
Units 1, 2, and 3 will use high-throughput transcriptome analysis (RNA-seq) based on quantitative next-generation sequencing (NGS) technologies, with the aim to compare the transcript profiles of hyper-/hypo-pathogenic Leishmania strains. Mapping of reads to the L. donovani and L. major reference genomes will help to define (i) the density of reads associated to any open reading frame (ORF), (ii) transcripts generated by alternative trans-splicing events, (iii) the map of initiation sites of parasite-specific poly-cistronic transcription, and (iv) sense and antisense transcript abundance [3]. This analysis will allow revealing transcripts that are exclusively expressed in virulent Leishmania, and will thus allow important new insight into Leishmania pathogenicity mechanisms.. ...
Thioredoxin system plays an important role in antioxidative stress, thioredoxin 2 (Trx2) being one of the most important components in the thioredoxin system. The full-length cDNA sequence of thioredoxin 2 from Euphausia superba (EsTrx2) is 1276 bp and contain a 5′ untranslated region (UTR) of 94 bp, a 3′ UTR of 741 bp and an open reading frame (ORF) of 441 bp, encoding a putative protein of 146 a ...
Laborator Synevo. Informatii generale. Virusul hepatitei E (HEV), recent inclus in genul Hepevirus al familiei Hepeviridae, cauzeaza o infectie acuta, de obicei, autolimitanta. Este un virus sferic, lipsit de invelis, cu diametru de 27-34 nm, alcatuit dintr-un genom ARN monocatenar cu polaritate pozitiva. Sunt descrise 4 genotipuri majore si un singur serotip. Genomul prezinta 3 cadre de citire (open reading frames = ORF): ORF1 codifica metiltransferaza, proteaza, helicaza si replicaza; ORF 2 codifica proteina capsidei; ORF3 codifica o proteina a carei functie nu a fost definita4.. HEV se transmite pe cale fecal-orala; consumul de apa potabila contaminata cu fecale este responsabil de aparitia majoritatii epidemiilor. Transmiterea directa de la o persoana la alta este neobisnuita. Transmiterea pe cale sexuala sau prin transfuzii nu a fost dovedita1;4.. Hepatita cu virus hepatitic E este endemica in Asia de sud-est si centrala, cu mai multe focare in Orientul Mijlociu, Africa de nord si de vest ...
防御素(defensins)是一类在先天性免疫系统中起着重要作用的阳离子抗菌肽。因其在机体抵御病原入侵方面起着重要作用,固命名为防御素。防御素对许多病原微生物有着天然的抵抗活性,包括病毒和细菌。目前,几个跟防御素的转录调控相关的转录因子已经被鉴定,如NF-κB、NF-IL6等。在本论文中,我们主要就青鳉防御素的基因功能及转录调控进行研究。首先,我们运用3′, 5′末端快速扩增法 (Rapid Amplification of cDNA Ends techniques, RACE)在青鳉(Oryzias latipes)眼睛中克隆到一个新的β-防御素基因,命名为OlBD。该基因的cDNA全长480bp,其中5′端和3′端非翻译区(Untranslated region,UTR)分别为68bp和240bp,在3′ 末端还含有一个典型的加尾信号(ATTAA)和26bp的多聚腺嘌呤尾(poly A 尾)。在该cDNA中的189bp 的开放阅读框(open reading frame,ORF) 编码了63个氨基酸(aa)的多肽。Southern blot ...
Researchers from IBCh RAS together with their international collаborators discovered an evolutionary link between efficiency of start codons and the probability of AUG codon occurrence in the 5'-end parts of protein-coding sequences. When start codons are inefficient the next AUG codon is more likely to be found in the same reading frame. At the same time in case of highly efficient start codons, the next AUG codon is more likely to be found in alternative frames. They also have shown that weak initiation at the first starts is associated with the synthesis of shortened proteoforms as a result of initiation at the second starts.
Reading follow up activities with AFs on by butterbeer. 28/08/2012 · Year 2 Guided Reading- Help! Guided Reading with me ICT activities like the independent reading, creative writing box, or a guided reading follow up …, Guided reading follow up activities linked to AFs on APP grid. Mostly for level 2, some level 1 and 3. The AF refs are for my benefit as they let me quickly choose a. ... was mapping out my guided reading lesson plans and activities. to follow the guided reading model ready to go guided reading lesson Use them to specify activities for pupils to complete, Guided Reading Follow-Up Question Cards Printable book covers for your Guided Reading books or folders.. The final activity on students guided reading schedules of our guided reading rotations minutes for guided reading. Let me know what you come up This guided reading aide includes a lesson plan for each of the 5 stories, follow up writing and drawing activities and a variety of questions to ask before, during. These study ...
Bacterial genomes serve as a blueprint in all aspects of biological research, and therefore accurate genome annotation is of paramount importance. However, increasing evidence indicates that currently annotated bacterial genomes have missed many genes encoding small proteins ≤60 aa (Wood et al. 2012; Warren et al. 2010). A small gene, or a small open reading frame (sORF), has previously been defined as one encoding proteins of ≤60 aa (Hemm et al. 2010); or alternatively, it accommodates those up to 100 aa (Andrews and Rothnagel 2014). While small proteins have been increasingly reported for their important cellular roles in bacteria (Alix and Blanc-Potard 2008; Martin et al. 2015; Hobbs et al. 2012), studies on small proteins are limited, partly because many small genes are unannotated in sequenced bacterial genomes (Alix and Blanc-Potard 2009; Storz et al. 2014). Despite much effort made to improve gene annotation, the accurate identification of small genes has been a persistent challenge ...
Plants respond to changes in sugar concentrations by altering their transcriptional profile and their metabolic processes. Sucrose triggers the translational repression of the transcription factor bZIP11 in Arabidopsis thaliana. Rahmani et al. show that this repression requires the 5′-leader sequence of bZIP11, which, when transferred to a reporter gene, decreased the expression of the reporter gene product (luciferase) in response to sucrose, consistent with sugar-induced translational repression. Deletion analysis revealed that the second upstream open reading frame (uORF2) was required. When the mRNA sequence of uORF2 was mutated without affecting the encoded peptide, sugar-induced translational repression occurred. Transplantation of the 82 nucleotides of the uORF2 sequence into the promoter of a gene not normally regulated by sucrose caused the production of the reporter gene to decrease in response to sucrose. Mutation of the encoded peptide, or changing the length of the encoded ...
The present invention relates to a method for transmitting a signal using a frame having a predetermined CP (Cyclic Prefix) length in a wireless communication system. The method includes receiving a signal from a base station using a first frame, and transmitting the signal to the base station using the first frame. Wherein the first frame is a frame supported by a first cell among the plurality of cells and the first frame is a frame different from a second frame supported by a second cell among the plurality of cells, An area where an uplink area of a first frame overlaps with a downlink area of the second frame or an area where a downlink area of the first frame overlaps with an uplink area of the second frame is punctured, The length of the CP of the first frame and the CP length of the second frame are different from each other. Frame, Cyclic Prefix, Interference
Gene expression during development is regulated both transcriptionally and translationally; however, relatively few examples of translational regulation are known. On p. 3575, Imai and colleagues describe for the first time how an upstream open reading frame (uORF) mediates translational control during plant development. Loss-of-function mutants of Arabidopsis ACAULIS 5 (ACL5), which encodes spermine synthase, have a dwarf phenotype because of a defect in stem elongation. To find out how ACL5 regulates stem elongation, the researchers isolated a dominant suppressor mutant of the acl5 phenotype - sac51-d. They show that sac51-d disrupts a short uORF of SAC51, which encodes a bHLH transcription factor. Other experiments indicate that this disruption might increase the translation of SAC51. Thus, the researchers suggest that the uORF-encoded protein normally prevents the initiation of SAC51 translation, and that ACL5 acts directly or indirectly (possibly through spermines effects on protein ...
This month the Open Knowledge Foundation is five years old.. Over those last five years weve done much to promote open access to information - from sonnets to stats, genes to geodata - not only in the form of specific projects like Open Shakespeare and Public Domain Works but also in the creation of tools such as KnowledgeForge and the Comprehensive Knowledge Archive Network, standards such as the Open Knowledge Definition, and events such as OKCon, designed to benefit the wider open knowledge community. (More about what weve been up just over the last year can be found in our latest annual report).. While we have achieved a lot, we believe we can do much, much more. We are therefore reaching out to our community and asking you to help us take our vision further.. Our aim: at least a 100 supporters committed to making regular, ongoing donations of £5 (EUR 6, $7.50) or more a month.. These funds will be essential in expanding and sustaining our work by allowing us to invest in infrastructure ...
This gene encodes an endonuclease that specifically degrades the RNA of RNA-DNA hybrids and is necessary for DNA replication and repair. This enzyme is present in both mitochondria and nuclei, which are resulted from translation of a single mRNA with two in-frame initiation start codons. The use of the first start codon produces the mitochondrial isoform and the use of the second start codon produces the nuclear isoform. The production of the mitochondrial isoform is modulated by an upstream open reading frame (uORF) which overlaps the first initiation start codon in human. An alternately spliced transcript variant has been found which encodes a shorter isoform. This gene has three pseudogenes; two of them are at different locations of chromosome 17 and one of them is on chromosome 1q32.2. [provided by RefSeq, Sep 2014 ...
Although nonsense mutations have been associated with the skipping of specific constitutively spliced exons in selected genes, notably the fibrillin gene, the basis for this association is unclear. Now, using chimaeric constructs in a model in vivo expression system, premature termination codons are …
A network system in which administrators of frame relay networks can recognize the quality of the ATM network suitably and manage the frame relay networks in accordance with the quality condition of the ATM network. When a frame F is transmitted from a frame relay network FR1 at a transmitting side to an IWF, a frame header in which a transmission number is stored is added to the frame F. Then, the frame F is received by a frame relay network FR2 at a transmitted side through the IWF and the ATM network. In the frame relay network FR2, a difference between the transmission number stored in the frame header of the frame F and a reception condition variable kept in the frame relay network FR2 is calculated, and the difference is stored in a quality information collection table as a number of discarded frames in the ATM network.
Greetings, faithful readers! Im sure you have both been wondering why the long hiatus - lots of reasons, mostly to do with laziness, but theres one in particular I need to get out of the way right away. I promised myself that I wouldnt say anything on the blog until Id corrected an error - and promptly stopped blogging for about two years!. But now I have things I want to talk about again, so its time (OK, way past time!) to do the necessary update.. In these two posts, I relied heavily on an NIH estimate of author-side charges, using it to calcluate page and colour charges on the basis of the assumption that most toll-access journals charge these.. On liblicense-L, Anthony Watkinson took me to task for that assumption, pointing out that it did not accord with his many years of experience as a publisher and going to the trouble of soliciting opinion from colleagues with similar backgrounds (all of whom agreed with him).. At the time, I could do no more than cede Anthonys point that my ...
The worlds first wiki where authorship really matters. Due credit and reputation for authors. Imagine a global collaborative knowledge base for original thoughts.
The worlds first wiki where authorship really matters. Due credit and reputation for authors. Imagine a global collaborative knowledge base for original thoughts.
sORFs.org datasets. This section provides detailed information about the datasets used. For more information about the dataset processing please consult the INFO page. navigate through the datasets on the left to acquire more information about the corresponding dataset. ...
We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each clusters gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq ...
It finally happened. Yesterday, Genentech announced that they made a go decision to advance T-DM1 into a phase III trial. Although no official announcement is out as of yet, Genentechs President of Product Development, Sue Hellmann, left no doubt in her prepared remarks: Additionally, we recently made a Phase III go decision for T-DM1 in…
Calculates entropy of the reads coverage over each grl group. The entropy value per group is a real number in the interval (0:1), where 0 indicates no variance in reads over group. For example c(0,0,0,0) has 0 entropy, since no reads overlap.
BiTE Antibodies A BiTE (Bispecific T Cell Engager) antibody is a bi-specific antibody (bsAb) which directs T-cells to attack cancer cells, by simultaneously binding the two cells. Upon binding, a physical link is created between the two cells, which in turn triggers the T cell to attack the target cell. Every BiTE antibody has two…
The genome has 67 open reading frames. Viral replication is cytoplasmic. Entry into the host cell is achieved by adsorption ...
The genome has three open reading frames. This has been studied by examining the ORF1 and the capsid proteins. The ORF1 protein ...
The genome has 2 open reading frames. Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration ...
They usually encode two open reading frames (ORF). The first ORF named gag is related to viral structural proteins. The second ... Exon shuffling follows certain splice frame rules. Introns can interrupt the reading frame of a gene by inserting a sequence ... There are three models of gene capture by helitrons: the 'read-through" model 1 (RTM1), the 'read-through" model 2 (RTM2) and a ... or be deleted without changing the reading frame.[2] ... It is composed of the read-through Helitron element and its ...
Its genome is 38,760 base pairs long with 65.3% of GC content and 5′-extruding cohesive ends; contains 51 open reading frames. ...
The genome has 1 or 2 open reading frames. Viral replication is cytoplasmic. Replication follows the double-stranded RNA virus ...
C3orf14-Chromosome 3 open reading frame 14: predicted DNA binding protein.. *C3orf23: encoding protein Uncharacterized protein ... Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. .. ... C3orf1: chromosome 3 open reading frame 1. *C3orf70 chromosome 3 open reading frame 70 ...
There are 11 open reading frames. Segments 1-3 encode viral proteins (VP)1-3, segments 4,7,8,9 and 11 code for non-structural ...
It encodes nine open reading frames. Two of these encode the structural proteins VP3 and VP4. Another (VP8) seems likely to be ...
The genome has 2 open reading frames. Entry into the host cell is achieved by penetration into the host cell. Replication ...
The G+C content is 68.4%. It encodes 56 open reading frames (ORFs). The structural proteins correspond to the ORFs as follows: ...
The genome has 2 open reading frames. Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment to ...
The genome has 2 open reading frames. Viral replication is cytoplasmic. Entry into the host cell is achieved by virus remains ...
It has eight open reading frames (ORFs). VP3 and VP4 are encoded by ORF3 and ORF4 respectively. ORF1 is probably a replication ...
The genome has 911 open reading frames. Replication follows the DNA strand displacement model. DNA-templated transcription is ...
The genome has 160 open reading frames. Viral replication is nuclear. DNA-templated transcription is the method of ...
The genome contains two large open reading frames (ORF). The open reading frames do not overlap. The predicted amino acid ... of viruses is the presence of only one open reading frame in typical picornaviruses and two distinct open reading frames in ... The conformation changes that occur with TrV are most likely the flipping open of pentameric subunits of the capsid at the two- ...
The genome has 457 open reading frames. Dna templated transcription is the method of transcription. Amoeba serve as the natural ...
There are three open reading frames (ORFs). The largest open reading frame lies toward the 5' end of the genome and encodes a ... The function of the two smaller open reading frames is not known but they appear to be envelope proteins. This taxon was first ...
The genome has three open reading frames. Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment ...
Meng, XJ; Paul, PS; Halbur, PG; Morozov, I (Dec 1995). "Sequence comparison of open reading frames 2 to 5 of low and high ... The genome contains nine open reading frames. PRRSV is a member of the genus Arterivirus, family Arteriviridae, order ...
The genome has 3 open reading frames. Viral replication is nuclear/cytoplasmic. Replication follows the dsDNA(RT) replication ...
The genome has 7 open reading frames. Viral replication is nuclear. Entry into the host cell is achieved by attachment of the ...
The genome has 108 open reading frames. Viral replication is nuclear. DNA-templated transcription is the method of ...
Only a partial sequence of XRV was isolated from the fruit bat, but based on its open reading frame it was identified as a ... ISBN 978-1-904455-21-9. MicrobiologyBytes - Reoviruses "Translation and Open Reading Frames". NCBI ORF finder - A web based ...
The genome has 72 open reading frames. Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment of ...
It has only two open reading frames. The 3' open reading frame is the structural capsid protein, cap, which can be spliced to ...
Their genomes contain six open reading frames. Of these, only two have been assigned a function: the putative nucleocapsid ...
It encodes 531 putative open reading frames. One of the proteins, WSSV449, has some similarity to host protein Tube and can ...
C16orf58: encoding protein Chromosome 16 open reading frame 58. *C16orf62: encoding protein Chromosome 16 open reading frame 62 ... C16orf96: encoding protein C16orf96, or chromosome 16 open reading frame 96,. *CARHSP1: Calcium-regulated heat stable protein 1 ... Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2.. ...
Furthermore, these computational models frame hypotheses that can be directly tested by biological or psychological experiments ... The first open international meeting focused on Computational Neuroscience was organized by James M. Bower and John Miller in ...
The general consensus is to perform surgery in late infancy, i.e. between six and twelve months.[42] Within this time frame the ... reading and spelling.[10] A decreased IQ may also be part of the problems.[10] ... This means that the neurocranium can only grow if the sutures remain open.[42] The neurocranium will not grow when the forces ... This intervention is likely most effective when used in the time frame between three and six months of age. ...
Further reading[edit]. *. Clark, George C., Jr.; Cain, J. Bibb (1981). Error-Correction Coding for Digital Communications. New ... "Digital Video Broadcast (DVB); Frame structure, channel coding and modulation for a second generation digital terrestrial ... In this context, there are various available Open-source software listed below (non exhaustive). ... "Digital Video Broadcast (DVB); Second generation framing structure, channel coding and modulation systems for Broadcasting, ...
Further reading. *. Bausell, R.B (2007). Snake oil science : the truth about complementary and alternative medicine. Oxford ... 2003). "Open versus hidden medical treatments: The patient's knowledge about a therapy affects the therapy outcome". Prevention ... Therapies are often framed as "natural" or "holistic", implicitly and intentionally suggesting that conventional medicine is " ... has created the opening into which alternative therapists have stepped. "People are told lies. There are 40 million websites ...
The dissolution of frame work grains and cements increases porosity particularly in sandstones.[3] ... Open main menu. Search. Clastic rock. * Read in another language * Watch this page ...
... was opened to the public on June 7, 1982. Priscilla's gamble paid off; after only a month of opening Graceland's ... Further reading[edit]. *Davidson, Linda Kay and David Gitlitz. Pilgrimage, from the Ganges to Graceland: An Encyclopedia (Santa ... with the adjoining Music Room behind a doorway framed by vivid large peacocks set in stained glass. The Music Room has a black ... It was opened to the public as a museum on June 7, 1982. The site was listed in the National Register of Historic Places on ...
PET scans are increasingly read alongside CT or magnetic resonance imaging (MRI) scans, with the combination (called "co- ... Saleh, H; Kassas, B (2015). "Developing Stereotactic Frames for Cranial Treatment". In Benedict, SH; Schlesinger, DJ; Goetsch, ... This includes the cost of the radiopharmaceutical and a stipend for the physician reading the scan.[69] ... As a result, both corrected and uncorrected images are always reconstructed and read together. ...
Tic214 is notable for being coded for by chloroplast DNA, more specifically the first open reading frame ycf1. Tic214 and Tic20 ... Multiple replication forks open up, allowing replication machinery to replicate the DNA. As replication continues, the forks ... gradients in deamination indicate that replication forks were most likely present and the direction that they initially opened ...
The entry of the U.S. into the War is also crucial to the time-frame proposed by Christian Gerlach, who argued in his 1997 ... The question of whether there was some coordination between the Lithuanian and Ukrainian militias remains open (i.e. ... He breaks this figure down into three categories: Ghettoization and general privation: over 800,000; open-air shootings: over ... which quickly opened the door to the systematic mass murder of European Jews.[30] For Hitler, Bolshevism was merely "the most ...
Open main menu. Search. Building. * Read in another language * Watch this page ... A timber-framed house in Marburg (Germany). A block of tenements (apartments) in Dresden (Germany) ...
It earned $4 million on its wide opening day on Friday.[47] During its wide opening weekend it earned $13.09 million from 3,006 ... The site's consensus reads, "Everest boasts all the dizzying cinematography a person could hope to get out of a movie about ... "Sony's Sizzling 'Spectre', 'Hotel Transylvania 2' Top Charts in Strong Frame - Intl Box Office Update". Deadline Hollywood ... 28.8 million from 5,154 screens from 36 markets opening at No. 1 in 12 countries.[40] IMAX comprised $3 million of the opening ...
Set in an open square, the building sits on massive columns that taper inwards as they rise. The elevation consists of ... He spent two years doing so and during that time, he read extensively about western philosophy. Tange also enrolled in the film ... Tange conceived that this plaza (with its oversailing space frame roof) would connect the display spaces and create a setting ... The Yoyogi National Gymnasium is situated in an open area in Yoyogi Park on an adjacent axis to the Meiji Shrine. The gymnasium ...
The board warned of a further rise in costs because the airport will not open before 2017. The current time-cost frame is ... Further readingEdit. *. Kuhlmann, Bernd (1996). Schönefeld bei Berlin: 1 Amt, 1 Flughafen und 11 Bahnhöfe [Schönefeld near ... "Berlin airport's 2014 opening cancelled again". The Local. 8 January 2014.. *^ "BER öffnet vielleicht erst 2016" [BER may open ... As of May 2017, estimates suggested the airport could open in late 2018 or early 2019, but an opening in 2020 was not ruled out ...
After having read the pilot script, he called it a "page turner."[30] Lisa Zwerling, who also signed a deal with UMS, served as ... Martinez and his wife Christina (Lisa Vidal) meet with Sophia in an attempt to get her to open up about the airplane. The ... The show's pilot episode is told almost entirely in retroversions to three different time frames. According to Nick Wauters, ... Men posing as federal officials attempt to transfer Sean from Yuma to Washington, D.C., but open fire in the building; Sean ...
Further reading. *. Long PH (2013). Barrett S, ed. Chiropractic Abuse: An Insider's Lament. American Council on Science & ... are more open to mainstream views and conventional medical techniques, such as exercise, massage, and ice therapy.[21] ... IPA performance for the same health maintenance organization product in the same geography and time frame.[162] ... and hence they tend to be open to mainstream medicine.[21] Many of them incorporate mainstream medical diagnostics and employ ...
Further reading[edit]. *Collis, John (1984), Oppida, earliest towns north of the Alps, Department of Prehistory and Archaeology ... a timber frame nailed together, was the dominant form of rampart construction. Dump ramparts, that is earth unsupported by ... the extensive bank and ditch earthworks topped with palisades were constructed to close off the open western gap between these ...
Its structure comprised a wooden frame covered with heat-shrunk Solarfilm model aircraft film. The wing was built in three ... open-circuit) output voltage of approximately 29 V. The motors drive a 63 in (160 cm) two-bladed propeller via a 3:1 bicycle- ...
The Congress came up with an Agenda for Action which was framed by the Convention on the Rights of the Child.[37] ... commercially sexually exploited children than the 300,000 and far more than the 827 suggested by these two most widely read ...
Drop handlebar, carbon fibre tubing frame, wire spokes. UCI best human effort (1984-2014)[10][11] Date Rider Age Velodrome ... RIH superlight steel frame, drop handlebars, wire spokes.[14][15] 18 October 2000. Anna Wilson-Millward. 26. Vodafone Arena, ... Triathlon handlebar, Trek carbon fibre tubing frame, disc wheels,[31] chain on a 55/14 gear ratio.[32]. First attempt under the ... Triathlon handlebar, BMC carbon fibre tubing frame, disc wheels, chain on a 56/14 gear ratio.[36]. Beat Jack Bobridge's ...
Further reading[edit]. *. Aznar, José Camón (1950). Dominico Greco. Madrid: Espasa-Calpe. OCLC 459049719.. ... The Opening of the Fifth Seal (1608-1614, oil, 225 × 193 cm., New York, Metropolitan Museum) has been suggested to be the prime ... Ildefonso still survives on the lower center of the frame.[4] His most important architectural achievement was the church and ... Foundoulaki, Efi (24 August 1990). "Reading El Greco through Manet (in Greek)". Anti (445): 40-47.. ...
... once Illyana opened the gateway, he uses this computer to cast a spell holding it open. ... Damage Control #4 (frame story only). *What If (vol. 2) #6 (alt version) ... She claws his chest open as she laughs that he is too easy. He again tries to strike her with the sword but she turns human ... She does so and opens a gateway to Manhattan. N'astirh had kidnapped Wiz Kid of the X-Terminators and coerced him into building ...
These, in turn, open the way for the enhancement of working memory capacity, which subsequently opens the way for development ... Further readingEdit. *. Mascolo, Michael F. (2015). "Neo-Piagetian theories of cognitive development". International ... Gardner, H. (1983). Frames of mind. The theory of multiple intelligences. New York: Basic Books. ... Thus, each increase in mental power with age opens the way for the construction of concepts and skills up to the new level of ...
At the opening round in Japan, Hayden finished seventh while Rossi won the race.[7] But the race was marred by the death of ... His father jokes that the number was selected because it could still be read when he frequently ended up upside down in the ... Hayden's bicycle was found in the nearby ditch with its frame snapped in half.[182] Riccione Municipal Police are in possession ... At the season opening round in Qatar, Hayden finished in the exact same position as where he finished last year, which is in ...
Electrolysis cells can be either open cell or closed cell. In open cell systems, the electrolysis products, which are gaseous, ... and inside a certain frame of time). In 2006-2007, the ENEA started a research program which claimed to have found excess power ... Read in another language. Cold fusion. This article is about the Fleischmann-Pons claims of nuclear fusion at room temperature ... MIT Open Access Articles.. *. Biberian, Jean-Paul (2007), "Condensed Matter Nuclear Science (Cold Fusion): An Update" (PDF), ...
Further reading[edit]. *. Rohonyi, Réka (1996). Wat Phra Dhammakaya: A Refuge in the Midst of a Turbulent World - Analysis of a ... The Dhammakaya Open University and the kutis (residences) for monks are also located in the older sections.[326] ... Construction of a Spherical Skeleton Frame Structure by Precast Concrete Technology]. Journal of Thailand Concrete Association ... The building is open to visitors and pilgrims.[337]. *The Dining Hall of Khun Yay Archaraya Chandra Khonnokyoong: The Dining ...
Rigid-framed chairs are generally made to measure, to suit both the specific size of the user and their needs and preferences ... They can be used as both a wheelchair and a standing frame, allowing the user to sit or stand in the wheelchair as they wish. ... Manual wheelchairs often have two push handles at the upper rear of the frame to allow for manual propulsion by a second person ... This seat is then covered, framed, and attached to a wheelbase. A bariatric wheelchair is one designed to support larger ...
Legislation in Saskatchewan, Manitoba, Ontario, and Nova Scotia expressly or by judicial opinion has been read to allow for ... Together with the Austrian Ministry for Social Security, Generations and Consumer Protection, the Justice Ministry opened the ... gone on to include Court monitoring of the implementation of legislation and even the framing of guidelines in the absence of ... the Epic Systems opinion opened the door dramatically to the use of these waivers as a condition of employment, consumer ...
Further reading. *Samir Amin (October 2016). The Kurdish Question Then and Now, in Monthly Review, Volume 68, Issue 05 ... Attendees celebrated the occasion by lighting a ritual fire and beating the frame drum or 'daf'.[68] Awat Tayib, the chief of ... During the relatively open government of the 1950s in Turkey, Kurds gained political office and started working within the ... Between 1984 and 1999, the PKK and the Turkish military engaged in open war, and much of the countryside in the southeast was ...
Open Court. p. 369.. *^ a b Bobzien, Susanne (1998). Determinism and freedom in Stoic philosophy. Oxford University Press. ISBN ... Further reading. *Bischof, Michael H. (2004). Kann ein Konzept der Willensfreiheit auf das Prinzip der alternativen ... On that basis "... free will cannot be squeezed into time frames of 150-350 ms; free will is a longer term phenomenon" and free ... Having participants read articles that simply "disprove free will" is unlikely to increase their understanding of determinism, ...
... single-stranded RNA is around 11,000 nucleotides long and has a single open reading frame encoding a polyprotein. Host ...
The ORF Finder (Open Reading Frame Finder)[9] is a graphical analysis tool which finds all open reading frames of a selectable ... In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the ability to be translated. An ORF ... One common use of open reading frames (ORFs) is as one piece of evidence to assist in gene prediction. Long ORFs are often used ... "Open reading frame". U.S. National Library of Medicine. 2015-10-19. Retrieved 2015-10-22.. .mw-parser-output cite.citation{font ...
Noncanonical open reading frames are shown to be essential for cancer cell function. ... Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they ... Noncanonical open reading frames encode functional proteins essential for cancer cell survival. *John R. Prensner1,2,3. , ... Detecting actively translated open reading frames in ribosome profiling data. Nat. Methods 13, 165-170 (2016). ...
Homo sapiens chromosome 19 open reading frame 45 (C19orf45), mRNA. PA. BC029824.1. Homo sapiens chromosome 19 open reading ... Chromosome 19 open reading frame 45 (C19orf45). Human protein-coding gene C19orf45. Represented by 41 ESTs from 16 cDNA ... Homo sapiens chromosome 19 open reading frame 45, mRNA (cDNA clone MGC:35139 IMAGE:5168945), complete cds. PA. ... frame 45, mRNA (cDNA clone MGC:34744 IMAGE:5170600), complete cds. PA. ...
... one or more short upstream open reading frames (uORFs) precede the initiation codon of the main coding region ... Upstream open reading frames (uORFs) are cis‐acting RNA elements involved in translational regulation, which precede the ... Upstream Open Reading Frames and Human Genetic Disease. Cristina Barbosa, Universidade de Lisboa, Lisboa, Portugal Cláudia ... Brown CY, Mize GJ, Pineda M, George DL and Morris DR (1999) Role of two upstream open reading frames in the translational ...
C6orf141 chromosome 6 open reading frame 141 [Homo sapiens] C6orf141 chromosome 6 open reading frame 141 [Homo sapiens]. Gene ... chromosome 6 open reading frame 141provided by HGNC. Primary source. HGNC:HGNC:21351 See related. Ensembl:ENSG00000197261 Gene ... C6orf141 chromosome 6 open reading frame 141 [ Homo sapiens (human) ] Gene ID: 135398, updated on 18-Aug-2020 ...
An upstream open reading frame (uORF) is an open reading frame (ORF) within the 5 untranslated region (5UTR) of an mRNA. ... Calvo SE, Pagliarini DJ, Mootha VK (May 2009). "Upstream open reading frames cause widespread reduction of protein expression ... "Peptidomic discovery of short open reading frame-encoded peptides in human cells". Nature Chemical Biology. 9 (1): 59-64. doi: ... "Regulation of fungal gene expression via short open reading frames in the mRNA 5untranslated region". Molecular Microbiology. ...
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
Return only the longest matches in re.finditer when identifying an Open Reading Frame ... I wish to run this for three frames. As mentioned earlier the three frames would be considering the first, second and third ... The two for-loops create the 6 different frames. The inner for-loop translates each frame according to the chosen translation ... how can i find the multiple substrings in one reading frame - Nodnin Oct 29 12 at 1:33 ...
Arrows indicate open reading frames. Extent of deletion constructs that eliminate cross-hybridizing genes are noted (ΔI and ... Telomeric Silencing of an Open Reading Frame in Saccharomyces cerevisiae Message Subject (Your Name) has forwarded a page to ... Telomeric Silencing of an Open Reading Frame in Saccharomyces cerevisiae. Arnold B. Barton and David B. Kaback ... Telomeric Silencing of an Open Reading Frame in Saccharomyces cerevisiae. Arnold B. Barton and David B. Kaback ...
Upstream open reading frames (uORFs) are common features of eukaryotic genes, occurring in 10%-25% of 5 leader sequences. ... Open Reading Frames, Protein Biosynthesis, Regulatory Sequences, Nucleic Acid, Selection, Genetic, Sequence Analysis, DNA. ...
Pervasive functional translation of noncanonical human open reading frames. By Jin Chen, Andreas-David Brunner, J. Zachery ... Pervasive functional translation of noncanonical human open reading frames. By Jin Chen, Andreas-David Brunner, J. Zachery ... Pervasive functional translation of noncanonical human open reading frames Message Subject. (Your Name) has forwarded a page to ... We find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical ...
... are open reading frames located within the 5 UTR of an mRNA. It is believed that translated uORFs reduce the translational ... Upstream open reading frames (uORFs) are open reading frames located within the 5 UTR of an mRNA. It is believed that ... von Arnim, A.G., Jia, Q., Vaughn, J.N.: Regulation of plant translation by upstream open reading frames. Plant Science: an ... Calvo, S.E., Pagliarini, D.J., Mootha, V.K.: Upstream open reading frames cause widespread reduction of protein expression and ...
Chromosome 1 open reading frame 194 (C1orf194) is a gene from Homo sapiens. The function of the protein coded by the gene is ... "C1orf194 chromosome 1 open reading frame 194 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-02-19 ...
types Specify regions which should be searched for open reading frames, e.g. LTR_retrotransposon -allorfs search for all ORFs ... gt-orffinder - Identifies ORFs (open reading frames) in sequences. SYNOPSIS. gt orffinder [option ...] indexname [GFF3_file ...
Upstream open reading frames: molecular switches in (patho)physiology View in MDC Repository ... Conserved upstream open reading frames (uORFs) are found within many eukaryotic transcripts and are known to regulate protein ...
Compare chromosome 9 open reading frame 173 Biomolecules from leading suppliers on Biocompare. View specifications, prices, ... Your search returned 2 chromosome 9 open reading frame 173 Biomolecules across 2 suppliers. ... We used this kit for efficient DNA digestion to inorder to obtain pure, high quality RNA which was ... read more ... I am studying a protein that is usually responsible for male gonad differentiation in mammals but is... read more ...
KudoZ) English to Polish translation of complete open reading frame of a cDNA molecule: otwarta ramka odczytu (cząsteczki cDNA ... complete open reading frame of a cDNA molecule. Polish translation: otwarta ramka odczytu (cząsteczki cDNA). ... complete open reading frame of a cdna molecule. otwarta ramka odczytu cząsteczki cDNA ... open reading frame (of a cDNA molecule). Polish translation:. otwarta ramka odczytu (cząsteczki cDNA). ...
The presented work explores the regulatory influence of upstream open reading frames (uORFs) on gene expression in Trypanosoma ... Life cycle adapted upstream open reading frames (uORFs) in Trypanosoma congolense: A post-transcriptional approach to ... Life cycle adapted upstream open reading frames (uORFs) in Trypanosoma congolense: A post-transcriptional approach to ... Finanziert durch den Open-Access-Publikationsfonds 2018 der Deutschen Forschungsgemeinschaft (DFG) und der Westfälischen ...
Mercury Resistance in Bacillus cereusRC607: Transcriptional Organization and Two New Open Reading Frames. Amit Gupta, Le T. ... The order of genes in the completed mercury resistance determinant is operator-promoter 1 (O/P1) merR1 merT open reading frame ... The first gene (initially called open reading frame 1 [ORF1] but now renamed merR1) encodes the positively acting homodimeric ... Mercury Resistance in Bacillus cereusRC607: Transcriptional Organization and Two New Open Reading Frames ...
Complete sets of cloned protein-encoding open reading frames (ORFs), or ORFeomes, are essential tools for large-scale ... hORFeome v3.1: A Resource of Human Open Reading Frames Representing Over 10,000 Human Genes Genomics. 2007 Mar;89(3):307-15. ... Complete sets of cloned protein-encoding open reading frames (ORFs), or ORFeomes, are essential tools for large-scale ...
Upstream open reading frames (uORFs) are cis‐acting elements, located before or overlapped with the main coding ORF (mORF), ... Upstream open reading frames (uORFs) are cis‐acting elements, located before or overlapped with the main coding ORF (mORF), ... 2020a) An upstream open reading frame regulates vasculogenic mimicry of glioma via ZNRD1‐AS1/miR‐499a‐5p/ELF1/EMI1 pathway. ... Upstream open reading frames (uORFs) are cis‐acting translational regulatory elements present within the 5′ leader sequence of ...
Identify the open reading frame in the following DNA sequence, the protein that this gene encodes for, its function, and the ... Identify the open reading frame in the following DNA sequence, the protein that this gene encodes for, its function, and the ... Which do you think it is? What are the two amino acid elements that *must* be present in an open reading frame? (Hint: Where ... This solution explains how to identify an open reading frame given a DNA sequence in order to determine the protein sequence ...
2002). In these strains, each individual open reading frame (ORF) was replaced by the KanMX drug-resistance gene. This ... Ninety-Six Haploid Yeast Strains With Individual Disruptions of Open Reading Frames Between YOR097C and YOR192C, Constructed ... Ninety-Six Haploid Yeast Strains With Individual Disruptions of Open Reading Frames Between YOR097C and YOR192C, Constructed ... Ninety-Six Haploid Yeast Strains With Individual Disruptions of Open Reading Frames Between YOR097C and YOR192C, Constructed ...
... chromosome 11 open reading frame 91), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol. ... LOVD (Leiden Open Variation Database). LOVD - Leiden Open Variation Database. LOVD (Leiden Open Variation Database). LOVD 3.0 ... LOVD (Leiden Open Variation Database). Whole genome datasets. ... C11orf91 100131378 chromosome 11 open reading frame 91. Aliases ...
Tags: academic career, AIDS, alternative open reading frames, Alzheimers Disease, diabetes, evolution, eye disease, genetics, ... Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One ...
Circadian clock locus frequency: protein encoded by a single open reading frame defines period length and temperature ... Circadian clock locus frequency: protein encoded by a single open reading frame defines period length and temperature ... Circadian clock locus frequency: protein encoded by a single open reading frame defines period length and temperature ... Circadian clock locus frequency: protein encoded by a single open reading frame defines period length and temperature ...
So, no blogging for me, and I wont be reading much except research papers either. Ill copy all my science/OA RSS feeds to ...
I would be safe from this kind of thing, down here at the far end of the blogospheres long tail, but for the spousal unit and her irritating habit of having sociable friends. I appear to have married a popular person. Howd that happen ...
  • One common use of open reading frames (ORFs) is as one piece of evidence to assist in gene prediction . (wikipedia.org)
  • Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. (nature.com)
  • Protein translation outside of annotated open reading frames (ORFs) in messenger RNAs and within ORFs in long noncoding RNAs is pervasive. (sciencemag.org)
  • Identifies ORFs (open reading frames) in sequences. (ubuntu.com)
  • Complete sets of cloned protein-encoding open reading frames (ORFs), or ORFeomes, are essential tools for large-scale proteomics and systems biology studies. (nih.gov)
  • It has been well known that the amino acid sequences of these proteins contain several conserved motifs, and that the open reading frames (ORFs) which encode helicase-related proteins make up several gene families. (uniprot.org)
  • A group of genes regulated by arginine was found clustered in the order argF -ORF1- argC - argJ -ORF4 between other, as yet uncharacterized, open reading frames (ORFs). (asm.org)
  • Two spliced mRNAs are encoded by this locus, and they contain three open reading frames (ORFs): UL128, UL130, and UL131. (asm.org)
  • Four of the 68 varicella-zoster virus (VZV) unique open reading frames (ORFs), i.e. (asm.org)
  • However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response.Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition.Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products. (nih.gov)
  • Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition. (nih.gov)
  • A very simplistic first step at identifying possible genes is to look for open reading frames (ORFs). (biostars.org)
  • We have reported previously that a recombinant DNA vaccine consisting of four Ehrlichia ruminantium (Welgevonden) open reading frames (ORFs) known as the 1H12 cocktail provided protection against a virulent E. ruminantium (Welgevonden) needle challenge in sheep. (up.ac.za)
  • Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between large and small proteins translated from a same gene is unknown. (inserm.fr)
  • Initial annotation of the tobacco mitochondrial genome in 2005 identified numerous identifiable protein coding, tRNA, and rRNA genes plus 119 open reading frames (ORFs) with no clearly stated function. (mtsu.edu)
  • An upstream open reading frame (uORF) is an open reading frame (ORF) within the 5' untranslated region (5'UTR) of an mRNA. (wikipedia.org)
  • Nearly all resistant transcripts possess at least one efficiently translated upstream open reading frame (uORF) that represses translation of the main coding ORF under normal conditions. (nih.gov)
  • Analysis of 5' leader and upstream open reading frame (uORF)features in the resistant mRNAs. (nih.gov)
  • In many eukaryotic messenger ribonucleic acids (mRNAs) one or more short upstream open reading frames (uORFs) precede the initiation codon of the main coding region. (els.net)
  • Upstream open reading frames (uORFs) are cis ‐acting RNA elements involved in translational regulation, which precede the initiation codon of the main coding region. (els.net)
  • Upstream open reading frames (uORFs) are common features of eukaryotic genes, occurring in 10%-25% of 5' leader sequences. (broadinstitute.org)
  • Upstream open reading frames (uORFs) are open reading frames located within the 5' UTR of an mRNA. (springer.com)
  • Conserved upstream open reading frames (uORFs) are found within many eukaryotic transcripts and are known to regulate protein translation. (mdc-berlin.de)
  • The presented work explores the regulatory influence of upstream open reading frames (uORFs) on gene expression in Trypanosoma congolense. (uni-muenster.de)
  • Upstream open reading frames (uORFs) are cis ‐acting elements, located before or overlapped with the main coding ORF (mORF), that regulate cap‐dependent translation efficiency in a transcript‐specific manner. (els.net)
  • Upstream open reading frames (uORFs) are cis ‐acting translational regulatory elements present within the 5′ leader sequence of mRNAs. (els.net)
  • The 5′ leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. (plantphysiol.org)
  • Upstream open reading frames (uORFs) are translational reading frames present in the 5′ leaders of mRNAs. (plantphysiol.org)
  • Many (431) upstream open reading frames (uORFs) are found in alternate 5′ ends and are significantly enriched in transcripts produced during the salt response. (g3journal.org)
  • Upstream open reading frames (uORFs) are elements found in the 5'-region of an mRNA transcript, capable of regulating protein production of the largest, or major ORF (mORF), and impacting organismal development and growth in fungi, plants, and animals. (biomedcentral.com)
  • Upstream open reading frames (uORFs) initiate translation within mRNA 5′ leaders, and have the potential to alter main coding sequence (CDS) translation on transcripts in which they reside. (biomedcentral.com)
  • Translation can also initiate within 5′ leaders at upstream open reading frames (uORFS). (biomedcentral.com)
  • Upstream open reading frames (uORFs) are prevalent cis-regulatory sequence elements in the transcript leader sequences (TLSs) of eukaryotic mRNAs. (mdc-berlin.de)
  • Background: Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. (chalmers.se)
  • Upstream open reading frames (uORFs) are a common class of genetic elements and are widely recognized as constitutive regulatory elements that impinge on the translation of their associated physiological downstream open reading frames. (medenbachlab.de)
  • The order of genes in the completed mercury resistance determinant is operator-promoter 1 (O/P1) merR1 merT open reading frame 3 (ORF3) ORF4 merA O/P2 merR2 merB2 merB1 . (asm.org)
  • The first annotation of the sequence of 21q confirmed 127 genes, and predicted an additional 98 previously unknown "anonymous" genes (predictions (PREDs) and open reading frames (C21orfs)), which were foreseen by exon prediction programs and/or spliced expressed sequence tags. (sigmaaldrich.com)
  • Transcriptional mapping of the varicella-zoster virus regulatory genes encoding open reading frames 4 and 63. (asm.org)
  • There were 627 novel peptides associated with these open reading frames that mapped to a unique genomic coordinate placed within the start/stop points of previously annotated genes. (biomedcentral.com)
  • Genes within genes: independent expression of phage T4 intron open reading frames and the genes in which they reside. (elsevier.com)
  • Systematic identification, classification, and characterization of the open reading frames which encode novel helicase-related proteins in Saccharomyces cerevisiae by gene disruption and Northern analysis. (uniprot.org)
  • This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. (biomedcentral.com)
  • The cloning and expression of large sets of open reading frames and proteins requires the management and analysis of significant amounts of data. (biomedcentral.com)
  • The open reading frame sequences of the target proteins are subsequently used to automatically design PCR primers and proceed with the expression of the target proteins. (biomedcentral.com)
  • Project 1: Myelination plays a key role in both the developing CNS and repair from neurodegenerative diseases such as multiple sclerosis (MS). Previous work has suggested a role for the amphoterin-induced gene and open reading frame (AMIGO) family of proteins in this process. (bham.ac.uk)
  • A six-frame translation of the entire human genome was used as the query database to search for novel blood proteins in the data from the Human Proteome Organization Plasma Proteome Project. (biomedcentral.com)
  • We previously reported the existence of six alternative open reading frame proteins in WNV genome, one of which entitled WARF4 is exclusively restricted to the lineage I of the virus. (biomedcentral.com)
  • Recombinant Human Chromosome 16 Open Reading Frame 53 RECOMBINANT & NATURAL PROTEINS Human samples 80 % of the research is conducted on human samples. (antibody-antibodies.com)
  • GENTAUR suppliers human normal cells, cell lines, RNA extracts and lots of antibodies and ELISA kits to Human proteins as well as Recombinant Human Chromosome 16 Open Reading Frame 53 RECOMBINANT & NATURAL PROTEINS. (antibody-antibodies.com)
  • Takahashi, H., Takahashi, A., Naito, S., Onouchi, H.: BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome. (springer.com)
  • The UL37 open reading frame of the herpes simplex virus type 1 (HSV-1) DNA genome is located between map units 0.527 and 0.552. (curehunter.com)
  • The chloroplast genome of all higher plants encodes, in its large single-copy region, a conserved open reading frame of unknown function ( ycf3 ), which is split by two group II introns and undergoes RNA editing in monocotyledonous plants. (rupress.org)
  • To elucidate the function of ycf3 we have deleted the reading frame from the tobacco plastid genome by biolistic transformation. (rupress.org)
  • WNV genome is a positive single-stranded RNA of about 11 kb containing a single open reading frame flanked by two untranslated regions. (biomedcentral.com)
  • The genome of hCoV-NL63 comprises 27,553 nt and has a gene organization conserved in all CoV, i.e., gene 1a/b, spike (S), open reading frame 3 (ORF 3), envelope (E), membrane (M) and the nucleocapsid (N) gene. (biomedcentral.com)
  • Springfeld, C, Darai, G & Cattaneo, R 2005, ' Characterization of the tupaia rhabdovirus genome reveals a long open reading frame overlapping with P and a novel gene encoding a small hydrophobic protein ', Journal of Virology , vol. 79, no. 11, pp. 6781-6790. (elsevier.com)
  • The purpose of this study was to explore expression of putative open reading frames in the Nicotiana tabacum mitochondrial genome. (mtsu.edu)
  • The genome has 2 open reading frames. (wikipedia.org)
  • Vink, C. 2001-11-01 00:00:00 Rat cytomegalovirus (RCMV) open reading frame R44 is the homolog of human cytomegalovirus gene UL44, which encodes the DNA polymerase accessory protein. (deepdyve.com)
  • Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. (elsevier.com)
  • Chromosome 1 open reading frame 194 (C1orf194) is a gene from Homo sapiens. (wikipedia.org)
  • MBS9338636 is a ready-to-use microwell, strip plate ELISA (enzyme-linked immunosorbent assay) Kit for analyzing the presence of the chromosome 1 open reading frame 168 (C1orf168) ELISA Kit target analytes in biological samples. (mybiosource.com)
  • From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. (sigmaaldrich.com)
  • The RAP2C cDNA contains an open reading frame of 552 bp, encoding a putative protein of 183 amino acid residues. (usda.gov)
  • Two possible open reading frames with the sequences are highlighted. (wikipedia.org)
  • For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. (wikipedia.org)
  • For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. (biomedcentral.com)
  • It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes. (biomedcentral.com)
  • The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank. (biomedcentral.com)
  • Open reading frames of single protein sequences can also be retrieved directly from the GenBank web site by following the appropriate links in the HTML display of GenBank protein sequences. (biomedcentral.com)
  • Coderet extracts transcript, open reading frame and protein sequences from GenBank DNA sequence entries. (biomedcentral.com)
  • I am trying to read ORF from a list of sequences and identify the one with maximum length and cor. (biostars.org)
  • In molecular genetics , an open reading frame ( ORF ) is the part of a reading frame that has the ability to be translated. (wikipedia.org)
  • The researchers investigated the relative positions of the first (main) and subsequent AUG codons in human mRNAs and found that the probability of finding the second codon in different reading frames depends on the context of the first codon. (ibch.ru)
  • Since DNA is interpreted in groups of three nucleotides (codons), a DNA strand has three distinct reading frames. (wikipedia.org)
  • 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). (umassmed.edu)
  • When start codons are inefficient the next AUG codon is more likely to be found in the same reading frame. (ibch.ru)
  • At the same time in case of highly efficient start codons, the next AUG codon is more likely to be found in alternative frames. (ibch.ru)
  • Moreover, comparative analysis of the contexts of the start codons across the genomes of different vertebrate indicates that the low efficiency of the first start is associated with the high efficiency of the second start (when in the same reading frame). (ibch.ru)
  • By this we mean look in all six frames for long regions without stop codons - an ORF is just a region of nucleotides with no in frame stop codons. (biostars.org)
  • Hello, I need to find a start codon and all in frame stop codons related to that primary start co. (biostars.org)
  • One of them is a reading frame of 168 (tobacco) or 170 (maize) codons located in the large single-copy region of higher plant chloroplast genomes and interrupted by two group II introns. (rupress.org)
  • Referring to this remarkable feature, it was initially designated IRF168 (intron-containing reading frame of 168 codons) ( 28 ), but later renamed ycf3 (hypothetical chloroplast reading frame No. 3). (rupress.org)
  • These findings demonstrate that posttranscriptional regulation of elastin production in mature tissue is conferred by a specific element within the open reading frame of tropoelastin mRNA. (asm.org)
  • [3] A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions. (wikipedia.org)
  • This represents the first demonstration that a human tumor rejection antigen can be generated from a normal cellular gene using an open reading frame other than that used to encode the normal protein. (rupress.org)
  • After termination, the 40S ribosomal subunits quickly reacquire a new ternary complex and reinitiate translation at uORF2, which overlaps out‐of‐frame with ATF4 mORF. (els.net)
  • We report that eIF3 and the small ribosomal subunit bind HIV RNA within gag open reading frame. (surrey.ac.uk)
  • Identification and characterization of the herpes simplex virus type 1 protein encoded by the UL37 open reading frame. (curehunter.com)
  • In the following years, most of these open reading frames could be assigned to functional gene products involved in either genetic system functions or in photosynthesis. (rupress.org)
  • The term "completeness" in GenBank sequence entries refers to a biomolecule, a clone, or a biological entity as gene, transcript or open reading frame. (biomedcentral.com)
  • Applying a false discovery rate threshold of 0.05, we identified 282 significant open reading frames, each containing two or more peptide matches. (biomedcentral.com)
  • Instead, this nonamer peptide resulted from translation of an alternative open reading frame of the same gene. (rupress.org)
  • When the start codon of the protein coding open reading frame is not in the optimal context, there are two possibilities for "leaky" ribosomes. (ibch.ru)
  • High throughput tandem mass spectrometry based proteomics provides an important new source of information to help define both the location of transcription units and the reading frame of protein translation. (biomedcentral.com)
  • Jeon, S., Kim, J.: Upstream open reading frames regulate the cell cycle-dependent expression of the RNA helicase Rok1 in Saccharomyces cerevisiae. (springer.com)
  • abstract = "The td, nrdB, and sunY introns of bacteriophage T4 each contain a long open reading frame (ORF). (elsevier.com)
  • Calvo, S.E., Pagliarini, D.J., Mootha, V.K.: Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. (springer.com)
  • Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans" (PDF). (wikipedia.org)
  • Chromosome 19 Open Reading Frame 10 Mouse Recombinant produced in E.Coli is a single, non-glycosylated, polypeptide chain containing 143 amino acids and having a molecular mass of 15.8kDa. (neobiolab.com)
  • Example of a six-frame translation. (wikipedia.org)
  • Morris, D.R., Geballe, A.P.: Upstream open reading frames as regulators of mRNA translation. (springer.com)
  • Error with frame/translation in BioPython? (biostars.org)
  • The Reading Frame Checker allows you to to quickly generate a prediction of the effect of whole-exon deletions and duplications on the RNA translation. (le.ac.uk)
  • MerR is a positively acting regulatory protein that binds to the transcriptional mRNA start site, and on addition of Hg 2+ , MerR twists and bends the DNA to a conformation suitable for opening and initiation of mRNA synthesis ( 1 , 30 ). (asm.org)
  • The location of the point mutation in the AD169 UL131 gene is indicated, and the portion of UL131 that is not expressed is designated by an open box. (asm.org)
  • We then investigated whether ICP0 expression in latently infected ganglia is reduced by the latency-associated transcripts (LATs) and whether splicing of ICP0 transcripts is inhibited by the product of open reading frame (01117) P. A LAT deletion mutation which essentially eliminates expression of the major LATs did not appreciably increase levels of ICP0 transcripts. (harvard.edu)
  • Presents an analysis of differential gene expression between prostate cancer and normal prostate tissues using complementary DNA microarray of open-reading frame expressed sequence tags (ORESTES). (ebscohost.com)
  • Your search returned 2 chromosome 9 open reading frame 173 Biomolecules across 2 suppliers. (biocompare.com)
  • First, the reading frame is conserved in all land plant chloroplast genomes ( 15 ) and displays a high degree of DNA homology as well as putative protein sequence homology ( 23 ). (rupress.org)
  • Raw data are available in the Source data files accompanying this manuscript, as well as through the NCBI Sequence Read Archive at: SRR13126801, SRR13128583, SRR13132373, SRR13142215 and SRR13142421. (nature.com)
  • -types Specify regions which should be searched for open reading frames, e.g. (ubuntu.com)
  • Instead, two unique terminal regions of about 6 kb and 12 kb rich in open reading frames with no homologs in mammalian adenoviruses could be found. (biomedcentral.com)
  • Our study focuses on hCoV-NL63 open reading frame 3 (ORF 3) which is a highly conserved accessory protein among coronaviruses. (biomedcentral.com)
  • If the next starting codon is in the same reading frame, then as a result of its recognition, the ribosome will synthesize a shortened version of the protein. (ibch.ru)
  • Role of a short open reading frame in ribosome shunt on the cauliflower mosaic virus RNA leader. (semanticscholar.org)
  • If the next starting codon is in one of the two other reading frames, a completely different polypeptide will be synthesized. (ibch.ru)
  • This tool identifies all open reading frames using the standard or alternative genetic codes. (wikipedia.org)
  • Amongst others, the script will check if the given deletion or duplication is in-frame or out-of-frame. (le.ac.uk)