Codon
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).
Codon, Initiator
Codon, Terminator
Base Sequence
RNA, Transfer, Met
Molecular Sequence Data
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.
Codon, Nonsense
An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.
Peptide Chain Initiation, Translational
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.
Protein Biosynthesis
RNA, Transfer
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Amino Acid Sequence
Mutation
Escherichia coli
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.
Anticodon
Caspases, Initiator
A subtype of caspases that contain long pro-domain regions that regulate the activation of the enzyme. The pro-domain regions contain protein-protein interaction motifs that can interact with specific signaling adaptor proteins such as DEATH DOMAIN RECEPTORS; DED SIGNALING ADAPTOR PROTEINS; and CARD SIGNALING ADAPTOR PROTEINS. Once activated, the initiator caspases can activate other caspases such as the EFFECTOR CASPASES.
Plasmids
Nucleic Acid Conformation
Replication Origin
A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Ribosomes
Genetic Code
RNA, Messenger
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.
Transcription, Genetic
TATA Box
Cloning, Molecular
DNA-Binding Proteins
RNA, Transfer, Amino Acyl
Promoter Regions, Genetic
Hydroxymethyl and Formyl Transferases
Prokaryotic Initiation Factor-2
The largest of the three prokaryotic initiation factors with a molecular size of approximately 80 kD. It functions in the transcription initiation process by promoting the binding of formylmethionine-tRNA to the P-site of the 30S ribosome and by preventing the incorrect binding of elongator tRNA to the translation initiation site.
Peptide Initiation Factors
DNA Helicases
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
Binding Sites
DNA
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).
Genes
Sequence Homology, Nucleic Acid
Restriction Mapping
Prokaryotic Initiation Factor-3
A prokaryotic initiation factor that plays a role in recycling of ribosomal subunits for a new round of translational initiation. It binds to 16S RIBOSOMAL RNA and stimulates the dissociation of vacant 70S ribosomes. It may also be involved in the preferential binding of initiator tRNA to the 30S initiation complex.
Exons
Polymerase Chain Reaction
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.
Point Mutation
Methionine-tRNA Ligase
Eukaryotic Initiation Factor-1
Peptide Chain Termination, Translational
Caspases
A family of intracellular CYSTEINE ENDOPEPTIDASES that play a role in regulating INFLAMMATION and APOPTOSIS. They specifically cleave peptides at a CYSTEINE amino acid that follows an ASPARTIC ACID residue. Caspases are activated by proteolytic cleavage of a precursor form to yield large and small subunits that form the enzyme. Since the cleavage site within precursors matches the specificity of caspases, sequential activation of precursors by activated caspases can occur.
Sequence Analysis, DNA
Saccharomyces cerevisiae
Caspase 2
A long pro-domain caspase that contains a caspase recruitment domain in its pro-domain region. Activation of this enzyme can occur via the interaction of its caspase recruitment domain with CARD SIGNALING ADAPTOR PROTEINS. Caspase 2 plays a role in APOPTOSIS by cleaving and activating effector pro-caspases. Several isoforms of this protein exist due to multiple alternative splicing of its MESSENGER RNA.
N-Formylmethionine
Models, Genetic
RNA, Transfer, Amino Acid-Specific
Oligoribonucleotides
Protein Binding
DNA Primers
Benzoyl Peroxide
RNA, Bacterial
Peptide Chain Elongation, Translational
Mutagenesis, Site-Directed
Sequence Alignment
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.
Evolution, Molecular
Trans-Activators
Caspase 9
A long pro-domain caspase that contains a caspase recruitment domain in its pro-domain region. Caspase 9 is activated during cell stress by mitochondria-derived proapoptotic factors and by CARD SIGNALING ADAPTOR PROTEINS such as APOPTOTIC PROTEASE-ACTIVATING FACTOR 1. It activates APOPTOSIS by cleaving and activating EFFECTOR CASPASES.
Sequence Homology, Amino Acid
Thromboplastin
Transcription Factors
Genes, ras
Family of retrovirus-associated DNA sequences (ras) originally isolated from Harvey (H-ras, Ha-ras, rasH) and Kirsten (K-ras, Ki-ras, rasK) murine sarcoma viruses. Ras genes are widely conserved among animal species and sequences corresponding to both H-ras and K-ras genes have been detected in human, avian, murine, and non-vertebrate genomes. The closely related N-ras gene has been detected in human neuroblastoma and sarcoma cell lines. All genes of the family have a similar exon-intron structure and each encodes a p21 protein.
Caspase 8
A long pro-domain caspase that contains a death effector domain in its pro-domain region. Caspase 8 plays a role in APOPTOSIS by cleaving and activating EFFECTOR CASPASES. Activation of this enzyme can occur via the interaction of its N-terminal death effector domain with DEATH DOMAIN RECEPTOR SIGNALING ADAPTOR PROTEINS.
HeLa Cells
Eukaryotic Initiation Factor-2
Gene Expression Regulation, Bacterial
Suppression, Genetic
Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).
Introns
Caspase 10
A long pro-domain caspase that contains a death effector domain in its pro-domain region. Activation of this enzyme can occur via the interaction of its N-terminal death effector domain with DEATH DOMAIN RECEPTOR SIGNALING ADAPTOR PROTEINS. Caspase 10 plays a role in APOPTOSIS by cleaving and activating EFFECTOR CASPASES. Several isoforms of this protein exist due to multiple alternative splicing of its MESSENGER RNA.
Peptide Termination Factors
Conserved Sequence
Transfection
5' Untranslated Regions
Transcription Factor TFIID
The major sequence-specific DNA-binding component involved in the activation of transcription of RNA POLYMERASE II. It was originally described as a complex of TATA-BOX BINDING PROTEIN and TATA-BINDING PROTEIN ASSOCIATED FACTORS. It is now know that TATA BOX BINDING PROTEIN-LIKE PROTEINS may take the place of TATA-box binding protein in the complex.
Gene Expression Regulation
Oligonucleotides
Proteins
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.
Origin Recognition Complex
Oligodeoxyribonucleotides
DNA Restriction Enzymes
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.
Amino Acyl-tRNA Synthetases
Apoptosis
One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.
Mutagenesis
Regulatory Sequences, Nucleic Acid
Replicon
Species Specificity
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.
Reading Frames
Carcinogens
Caspase Inhibitors
Papilloma
Operon
Alleles
Transcription Initiation Site
Polymorphism, Genetic
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
DNA, Complementary
Reticulocytes
Immature ERYTHROCYTES. In humans, these are ERYTHROID CELLS that have just undergone extrusion of their CELL NUCLEUS. They still contain some organelles that gradually decrease in number as the cells mature. RIBOSOMES are last to disappear. Certain staining techniques cause components of the ribosomes to precipitate into characteristic "reticulum" (not the same as the ENDOPLASMIC RETICULUM), hence the name reticulocytes.
Selection, Genetic
DNA Footprinting
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Phenotype
Consensus Sequence
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.
Single-Strand Specific DNA and RNA Endonucleases
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.
RNA, Fungal
Protein Structure, Tertiary
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.
Models, Molecular
Genes, Reporter
Chromosome Mapping
Genes, Regulator
Recombinant Fusion Proteins
CRADD Signaling Adaptor Protein
Edeine
Oligonucleotide Probes
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.
Cell-Free System
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
Genotype
Apoptosomes
Multimeric protein complexes formed in the CYTOSOL that play a role in the activation of APOPTOSIS. They can occur when MITOCHONDRIA become damaged due to cell stress and release CYTOCHROME C. Cytosolic cytochrome C associates with APOPTOTIC PROTEASE-ACTIVATING FACTOR 1 to form the apoptosomal protein complex. The apoptosome signals apoptosis by binding to and activating specific INITIATOR CASPASES such as CASPASE 9.
Structure-Activity Relationship
Ribonuclease T1
Eukaryotic Initiation Factor-3
A multisubunit eukaryotic initiation factor that contains at least 8 distinct polypeptides. It plays a role in recycling of ribosomal subunits to the site of transcription initiation by promoting the dissociation of non-translating ribosomal subunits. It also is involved in promoting the binding of a ternary complex of EUKARYOTIC INITIATION FACTOR-2; GTP; and INITIATOR TRNA to the 40S ribosomal subunit.
Eukaryotic Cells
Polymerization
Gene Expression
Amino Acids
Guanosine Triphosphate
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Chromosomes, Bacterial
Electrophoresis, Polyacrylamide Gel
Photoinitiators, Dental
Chemical compound used to initiate polymerization of dental resins by the use of DENTAL CURING LIGHTS. It absorbs UV light and undergoes decomposition into free radicals that initiate polymerization process of the resins in the mix. Each photoinitiator has optimum emission spectrum and intensity for proper curing of dental materials.
Methylmethacrylate
Methylmethacrylates
Ribosomal Proteins
tRNA Methyltransferases
9,10-Dimethyl-1,2-benzanthracene
Nucleotides
Mitochondria
Semiautonomous, self-reproducing organelles that occur in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. They contain distinctive RIBOSOMES, transfer RNAs (RNA, TRANSFER); AMINO ACYL T RNA SYNTHETASES; and elongation and termination factors. Mitochondria depend upon genes within the nucleus of the cells in which they reside for many essential messenger RNAs (RNA, MESSENGER). Mitochondria are believed to have arisen from aerobic bacteria that established a symbiotic relationship with primitive protoeukaryotes. (King & Stansfield, A Dictionary of Genetics, 4th ed)
Repressor Proteins
Polymorphism, Single-Stranded Conformational
Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
Frameshifting, Ribosomal
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.
Polymethyl Methacrylate
Polymerized methyl methacrylate monomers which are used as sheets, moulding, extrusion powders, surface coating resins, emulsion polymers, fibers, inks, and films (From International Labor Organization, 1983). This material is also used in tooth implants, bone cements, and hard corneal contact lenses.
Virus Replication
Saccharomyces cerevisiae Proteins
Dimerization
RNA, Transfer, Gln
RNA
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)
Base Pairing
Pedigree
Potassium Permanganate
DNA, Recombinant
Methacrylates
Blotting, Northern
Genes, p53
Nanovirus
DNA, Single-Stranded
Sp1 Transcription Factor
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
RNA Splicing
Enzyme Activation
Nucleic Acid Hybridization
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)
RNA, Transfer, Ser
beta-Galactosidase
Prokaryotic Cells
Cells, Cultured
RNA, Transfer, Arg
Genes, Suppressor
Gene Expression Regulation, Viral
Phosphines
Protein Conformation
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).
Caspase 6
Alternative Splicing
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.
Peptide Elongation Factor Tu
A protein found in bacteria and eukaryotic mitochondria which delivers aminoacyl-tRNA's to the A site of the ribosome. The aminoacyl-tRNA is first bound to a complex of elongation factor Tu containing a molecule of bound GTP. The resulting complex is then bound to the 70S initiation complex. Simultaneously the GTP is hydrolyzed and a Tu-GDP complex is released from the 70S ribosome. The Tu-GTP complex is regenerated from the Tu-GDP complex by the Ts elongation factor and GTP.
Chloramphenicol O-Acetyltransferase
An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.
Methionyl Aminopeptidases
Rabbits
Mutagenesis, Insertional
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.
Machine learning approaches for the prediction of signal peptides and other protein sorting signals. (1/852)
Prediction of protein sorting signals from the sequence of amino acids has great importance in the field of proteomics today. Recently, the growth of protein databases, combined with machine learning approaches, such as neural networks and hidden Markov models, have made it possible to achieve a level of reliability where practical use in, for example automatic database annotation is feasible. In this review, we concentrate on the present status and future perspectives of SignalP, our neural network-based method for prediction of the most well-known sorting signal: the secretory signal peptide. We discuss the problems associated with the use of SignalP on genomic sequences, showing that signal peptide prediction will improve further if integrated with predictions of start codons and transmembrane helices. As a step towards this goal, a hidden Markov model version of SignalP has been developed, making it possible to discriminate between cleaved signal peptides and uncleaved signal anchors. Furthermore, we show how SignalP can be used to characterize putative signal peptides from an archaeon, Methanococcus jannaschii. Finally, we briefly review a few methods for predicting other protein sorting signals and discuss the future of protein sorting prediction in general. (+info)Exon shuffling by L1 retrotransposition. (2/852)
Long interspersed nuclear elements (LINE-1s or L1s) are the most abundant retrotransposons in the human genome, and they serve as major sources of reverse transcriptase activity. Engineered L1s retrotranspose at high frequency in cultured human cells. Here it is shown that L1s insert into transcribed genes and retrotranspose sequences derived from their 3' flanks to new genomic locations. Thus, retrotransposition-competent L1s provide a vehicle to mobilize non-L1 sequences, such as exons or promoters, into existing genes and may represent a general mechanism for the evolution of new genes. (+info)The chloroplast infA gene with a functional UUG initiation codon. (3/852)
All chloroplast genes reported so far possess ATG start codons and sometimes GTGs as an exception. Sequence alignments suggested that the chloroplast infA gene encoding initiation factor 1 in the green alga Chlorella vulgaris has TTG as a putative initiation codon. This gene was shown to be transcribed by RT-PCR analysis. The infA mRNA was translated accurately from the UUG codon in a tobacco chloroplast in vitro translation system. Mutation of the UUG codon to AUG increased translation efficiency approximately 300-fold. These results indicate that the UUG is functional for accurate translation initiation of Chlorella infA mRNA but it is an inefficient initiation codon. (+info)Involvement of the aphthovirus RNA region located between the two functional AUGs in start codon selection. (4/852)
Initiation of translation in picornavirus RNAs occurs internally, mediated by an element termed internal ribosome entry site (IRES). In the aphthovirus RNA, the IRES element directs translation initiation at two in-frame AUGs separated by 84 nucleotides. We have found that bicistronic constructs that contained the IRES element followed by the fragment including the aphthovirus start codons in front of the second gene mimicked the translation initiation pattern of viral RNA observed in infected cells. In those constructs, the frequency of initiation at the first AUG was increased by a sequence context that resembled the favorable consensus for cap-dependent translation, although initiation at the second site was always preferred. In addition, we have found that initiation at the second start codon was not diminished under conditions in which the first initiation codon was blocked by antisense oligonucleotide interference. Interestingly, mutations that positioned the second AUG out-of-frame with the first AUG did not interfere with the frequency of initiation at the second one. On the contrary, IRES-dependent translation initiation in bicistronic constructs lacking the sequences present between functional AUGs in the viral RNA was sensitive to the presence of out-of-frame initiator codons and hairpins in the spacer region. This remarkable difference in start codon recognition was due to the nucleotide composition of the RNA that separated the IRES from the initiator codon. Thus our results indicate that the region located in the aphthovirus RNA between functional AUGs is involved in start codon recognition, strongly favoring selection of the second start AUG as the main initiator codon. (+info)Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid. (5/852)
Replication of the IncL/M plasmid pMU604 is controlled by a small antisense RNA molecule (RNAI), which, by inhibiting the formation of an RNA pseudoknot, regulates translation of the replication initiator protein, RepA. Efficient translation of the repA mRNA was shown to require the translation and correct termination of the leader peptide, RepB, and the formation of the pseudoknot. Although the pseudoknot was essential for the expression of repA, its presence was shown to interfere with the translation of repB. The requirement for pseudoknot formation could in large part be obviated by improving the ribosome binding region of repA, either by replacing the GUG start codon by AUG or by increasing the spacing between the start codon and the Shine-Dalgarno sequence (SD). The spacing between the distal pseudoknot sequence and the repA SD was shown to be suboptimal for maximal expression of repA. (+info)Multiple murine double minute gene 2 (MDM2) proteins are induced by ultraviolet light. (6/852)
The mdm2 (murine double minute 2) oncogene encodes several proteins, the largest of which (p90) binds to and inactivates the p53 tumor suppressor protein. Multiple MDM2 proteins have been detected in tumors and in cell lines expressing high levels of mdm2 mRNAs. Here we show that one of these proteins (p76) is expressed, along with p90, in wild-type and p53-null mouse embryo fibroblasts, indicating that it may have an important physiological role in normal cells. Expression of this protein is induced, as is that of p90, by UV light in a p53-dependent manner. The p76 protein is synthesized via translational initiation at AUG codon 50 and thus lacks the N terminus of p90 and does not bind p53. In cells, p90 and p76 can be synthesized from mdm2 mRNAs transcribed from both the P1 (constitutive) and P2 (p53-responsive) promoters. Site-directed mutagenesis reveals that these RNAs give rise to p76 via internal initiation of translation. In addition, mdm2 mRNAs lacking exon 3 give rise to p76 exclusively, and such mRNAs are induced by p53 in response to UV light. These data indicate that p76 may be an important product of the mdm2 gene and a downstream effector of p53. (+info)Postsynaptic alpha-neurotoxin gene of the spitting cobra, Naja naja sputatrix: structure, organization, and phylogenetic analysis. (7/852)
The venom of the spitting cobra, Naja naja sputatrix contains highly potent alpha-neurotoxins (NTXs) in addition to phospholipase A2 (PLA2) and cardiotoxin (CTX). In this study, we report the complete characterization of three genes that are responsible for the synthesis of three isoforms of alpha-NTX in the venom of a single spitting cobra. DNA amplification by long-distance polymerase chain reaction (LD-PCR) and genome walking have provided information on the gene structure including their promoter and 5' and 3' UTRs. Each NTX isoform is approximately 4 kb in size and contains three exons and two introns. The sequence homology among these isoforms was found to be 99%. Two possible transcription sites were identified by primer extension analysis and they corresponded to the adenine (A) nucleotide at positions +1 and -45. The promoter also contains two TATA boxes and a CCAAT box. Putative binding sites for transcriptional factors AP-2 and GATA are also present. The high percentage of similarity observed among the NTX gene isoforms of N. n. sputatrix as well as with the alpha-NTX and kappa-NTX genes from other land snakes suggests that the NTX gene has probably evolved from a common ancestral gene. (+info)The cis acting sequences responsible for the differential decay of the unstable MFA2 and stable PGK1 transcripts in yeast include the context of the translational start codon. (8/852)
A general pathway of mRNA turnover has been described for yeast in which the 3' poly(A) tail is first deadenylated to an oligo(A) length, leading to decapping and subsequent 5'-3' exonucleolytic decay. The unstable MFA2 mRNA and the stable PGK1 mRNAs both decay through this pathway, albeit at different rates of deadenylation and decapping. To determine the regions of the mRNAs that are responsible for these differences, we examined the decay of chimeric mRNAs derived from the 5' untranslated, coding, and 3' untranslated regions of these two mRNAs. These experiments have led to the identification of the features of these mRNAs that lead to their different stabilities. The MFA2 mRNA is unstable solely because its 3' UTR promotes the rates of deadenylation and decapping; all other features of this mRNA are neutral with respect to mRNA decay rates. The PGK1 mRNA is stable because the sequence context of the PGK1 translation start codon and the coding region function together to stabilize the transcript, whereas the PGK13' UTR is neutral with respect to decay. Importantly, changes in the PGK1 start codon context that destabilized the transcript also reduced its translational efficiency. This observation suggests that the nature of the translation initiation complex modulates the rates of mRNA decapping and decay. (+info)
Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5
Al Shifa Hospital Gaza - Australian Broadcasting Corporation - Reporter Sarah Fergusson
Record details
Applications filed at Aug 04 2016 | STATIC PROGRAM ANALYSIS METHOD FOR DETECTING SECURITY BUGS IN PROGRAMS
THAT RELY ON...
Applications filed at Aug 31 2017 | CORNER FLASHING SYSTEM | Patents.com
Gene Ontology Classifications
c-myc antibody Mouse anti Human | CMYC Antibody | P64 Antibody | ProSpec
jwz: 18-Aug-2004 (Wed)
N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape...
A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia...
Start codon context and occurrence of AUG codons in the beginning of protein coding open reading frames co-evolve - Press-room ...
EIF3E - Early Detection Research Network
EIF3E - EDRN Public Portal
Gene Ontology Classifications
Prodigal - Mathematical software - swMATH
Function of the alternative proteome in neurodegenerative diseases | cettesemaine.utoronto.ca
20 Aug | Article about 20 Aug by The Free Dictionary
Patents filed at Aug 15 2017 | Controller of an electric motor | Patents.com
Patents filed at Aug 15 2017 | To apply a fluid to a substrate | Patents.com
American Urogynecologic Society (AUGS), AUGS Career Center|Find Your Career Here
American Urogynecologic Society (AUGS), AUGS Career Center|Find Your Career Here
initiation codon
environmental initiators | desencadeadores ambientais
CSIRO National Collections and Marine Infrastructure - Information and Data Centre
everlasting blort - jul 29 - aug 4, 2002
Translational control of Scamper expression via a cell-specific internal ribosome entry site<...
Measurements of translation initiation from all 64 codons in E. coli | Meta
Tour de France 2011: Synthetic testosterone in Landis sample
Prodigal: prokaryotic gene recognition and translation initiation site identification
Understanding initiation mechanisms and controlling properties of microtubule spools. (Conference) | SciTech Connect
What are codons? | Reference.com
What Are mRNA Codons? (with pictures)
Outsource Software Translation Services - Flatworld Solutions
Chemical aspects on the distribution of codons
miRNA Entry for MI0001145
Newsday.com Crossword Answers - Aug 12 2020 - crossword puzzle clues
In Touch - Aug. 31, 2007 - Daily Devotional
Anna Andress: 23-Aug-2011
miRNA Entry for MI0022481
KlezCalendar: Golem, Washington, DC, Aug 29
JQUERY, JSON , Angular and Less Interview questions - CodeProject
Aug 09 Rotation | Cathe Friedrich Fitness Forums
Alternate translation initiation on hepatitis B virus X mRNA produces multiple polypeptides that differentially transactivate...
Alternative initiation at a UUG codon gives rise to two functional variants of the mitochondrial protein Kgd4
Oral History | Life in Science | Advice to Young Scientists | Jerry Adams on Discovering the Initiation Mechanism for...
Quality - Practice Management | AUGS
Translation Efficiency
Patent US7820158 - Ligand-coupled initiator polymers and methods of use - Google Patents
WP Multilang Templates with Oxygen Builder
Kaysville Pioneer Honored by Many Standard 01Aug1913 - Newspapers.com
Fire and rescue calls for Aug. 20 - Page 143921 - Rappahannock News
Re: Discussion: what would not blocking on btrfs look like?
Features | LaRueCountyHerald.com
2016 SSC CGL Tier 1 28 Aug Shift - 3 | ExamVictor
GED orientation classes start Monday, Aug. 4
The latest numbers on COVID-19 in Canada for Aug. 12 | Times Colonist
iMedX Announces Acquisition of Worl... ( SHELTON Conn. Aug. ...)
Employee retention secrets revealed Aug. 24 - McKnights Long Term Care News
Georgia-Pacific to Distribute Second Quarter 2006 Financial Information on Aug. 15 | WebWire
SEATTLE, Aug. 7, 2007 LAWFUEL - The Legal Newswire -- Keller Rohrb...
Gervonta Davis, Nathan Cleverly to defend world titles on undercard of the Floyd Mayweather-Conor McGregor fight on Aug. 26 in...
Aug 20, 2009
How do I discuss new things I want to try? - Created by LaLaLouise on Aug 12, 2011: EdenFantasys Forum
Weekly Price Action & Technical Analysis Setups | Aug 11-16 - 2ndSkies Forex
3-methylmorphine for sale - Herbal Boilx (boils relief) - Aug 21, 2017
Weekly Forex Price Action Setups | Aug 4-9 - 2ndSkies Forex
Marilyn Kozak
Kozak, M (31 January 1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by ... Kozak, M (January 1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by ... Kozak, M (1981). "Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes". ... Kozak, Marilyn (1981-10-24). "Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ...
Invertebrate mitochondrial code
... a new initiator codon in vertebrate mitochondrial genome". Nucleic Acids Research. 16 (13): 6233. doi:10.1093/nar/16.13.6233. ... GUG may possibly function as an initiator in Drosophila. AUU is not used as an initiator in Mytilus "An exceptional mechanism ... Sengupta S, Yang X, Higgs PG (June 2007). "The mechanisms of codon reassignments in mitochondrial genetic codes". Journal of ... The codon AGG is absent in Drosophila. AUA, AUU AUC: Apis GUG: Polyplacophora UUG: Ascaris, Caenorhabditis. Nematoda: Ascaris, ...
Kozak consensus sequence
Kozak M (1984). "Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in ... At the AUG codon a Methionine tRNA anticodon is recognized by mRNA codon. Upon base pairing to the start codon the eIF5 in the ... Kozak, Marilyn (March 1984). "Point mutations close to the AUG initiator codon affect the efficiency of translation of rat ... Kozak M (1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ...
Translation initiation factor IF-3
It also allows for rapid codon-anticodon pairing for the initiator tRNA to bind quickly. IF3 is required by the small subunit ... The chloroplast homolog enhances the poly(A,U,G)-dependent binding of the initiator tRNA to its ribosomal 30s subunits. IF1-IF3 ... the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit. ...
Bacterial initiation factor
It also allows for rapid codon-anticodon pairing for the initiator tRNA to bind quickly to. IF3 is required by the small ... Bacterial initiation factor 2 binds to an initiator tRNA and controls the entry of that tRNA into the ribosome. IF2, bound to ...
Inferring horizontal gene transfer
Wuitschick JD, Karrer KM (1999). "Analysis of genomic G + C content, codon usage, initiator codon context and translation ... Codon usage bias, a measure related to codon frequencies, was one of the first detection methods used in methodical assessments ... This approach requires a host genome which contains a bias towards certain synonymous codons (different codons which code for ... for example the third nucleotide in a codon and the first nucleotide in the following codon represent the dinucleotide least ...
GC-content
Wuitschick JD, Karrer KM (1999). "Analysis of genomic G + C content, codon usage, initiator codon context and translation ... This has been pointed to the fact that the stop codon has a bias towards A and T nucleotides, and, thus, the shorter the ... Codon usage bias Definition of GC - content on CancerWeb of Newcastle University,UK Yakovchuk P, Protozanova E, Frank- ... Comparison of more than 1,000 orthologous genes in mammals showed marked within-genome variations of the third-codon position ...
TUBA4A
... exons either provide or deny an initiator methionine codon to the same alpha-tubulin coding region". Nucleic Acids Research. 15 ...
Nonsense suppressor
Start codons can also be suppressed with suppressor initiator tRNAs, such as the amber stop codon suppressor tRNAfMet2(CUA). ... In addition, many genes do not have only one termination codon, and cells commonly use ochre codons as the termination signal, ... Nonsense suppressors can be generally divided into two classes: a) a mutated tRNA which can bind with a termination codon on ... Genes with different or multiple stop codons will be unaffected. SUP35, a nonsense suppressor identified by Wickner in 1994, is ...
Transfer RNA
The amber initiator tRNA inserts methionine and glutamine at UAG codons preceded by a strong Shine-Dalgarno sequence. An ... Highly expressed genes seem to be enriched in codons that are exclusively using codons that will be decoded by these modified ... Once the A/A and P/P tRNAs have moved to the P/P and E/E sites, the mRNA has also moved over by one codon and the A/T site is ... The mRNA encodes a protein as a series of contiguous codons, each of which is recognized by a particular tRNA. One end of the ...
SUI1
... helped by eIF2 and the initiator Met-tRNAiMet. SUI1 ensures that translation initiation commences from the correct start codon ... SUI1 promotes a high initiation fidelity for the AUG codon, discriminating against non-AUG codons. In E. coli however, it seems ... and 2β discriminate against poor AUG context and non-AUG start codons". Molecular and Cellular Biology. 31 (23): 4814-31. doi: ... recognition of the start codon". Molecular and Cellular Biology. 12 (1): 248-60. doi:10.1128/mcb.12.1.248. PMC 364089. PMID ...
TPSB2
These genes have an intron immediately upstream of the initiator Met codon, which separates the site of transcription ...
Internal ribosome entry site
HCV-like IRESs directly bind the 40S ribosomal subunit to position their initiator codons are located in ribosomal P-site ...
Shine-Dalgarno sequence
The degree of base pairing also plays a role in determining the rate of initiation at different AUG initiator codons. In 1973 ... Once recruited, tRNA may add amino acids in sequence as dictated by the codons, moving downstream from the translational start ... Since this conserved sequence contained the complement of each of the three eukaryotic termination codons (UAA, UAG and UGA) it ... doi:10.1016/0092-8674(89)90122-0. Steitz J A, Jakes K (1975). "How ribosomes select initiator regions in mRNA: base pair ...
Glycine dehydrogenase (decarboxylating)
2005). "A single nucleotide substitution that abolishes the initiator methionine codon of the GLDC gene is prevalent among ...
Hepatitis C virus internal ribosome entry site
Moreover, it binds 40S in such a manner that AUG initiator codon is positioned in the ribosomal P-site, thus no ribosomal ... Initiator tRNA is delivered either by eIF2 or, in stress conditions when eIF2 is inactivated, by eIF2A, eIF2D, or possibly ... UTR to reach to start codon. In contrast, translation of hepatitis C virus (HCV) mRNA is initiated by a different mechanism ...
Central dogma of molecular biology
The ribosome reads the mRNA triplet codons, usually beginning with an AUG (adenine−uracil−guanine), or initiator methionine ... matching the codon in the mRNA to the anti-codon on the tRNA. Each tRNA bears the appropriate amino acid residue to add to the ... Translation ends with a stop codon which may be a UAA, UGA, or UAG triplet. The mRNA does not contain all the information for ... The encoding of proteins is done in groups of three, known as codons according to the table. In the sense that DNA replication ...
Eukaryotic translation
... the amino acid encoded by the start codon is methionine. The Met-charged initiator tRNA (Met-tRNAiMet) is brought to the P-site ... The initiator tRNA occupies the P site in the ribosome, and the A site is ready to receive an aminoacyl-tRNA. During chain ... At the end of the initiation step, the mRNA is positioned so that the next codon can be translated during the elongation stage ... Leaky termination in these genes leads to translational readthrough of up to 10% of the stop codons of these genes. Some of ...
TPSD1
... most of the tryptase genes have an intron immediately upstream of the initiator Met codon, which separates the site of ...
Bacterial, archaeal and plant plastid code
It is essentially the same as the standard code, however there are some variations in alternative start codons. A The codon AUG ... CUG is known to function as an initiator for one plasmid-encoded protein (RepA) in E. coli. In addition to the NUG initiations ... The other start codons listed by GenBank are rare in eukaryotes and generally codes for Met/fMet. B ^ ^ ^ The historical basis ... Golderer, G; Dlaska, M; Gröbner, P; Piendl, W (October 1995). "TTG serves as an initiation codon for the ribosomal protein ...
P-site
Initiation involves recognition of the start codon (AUG) by initiator tRNA in the P-site, elongation involves passage of many ... The A-site binds to incoming aminoacyl-tRNA which has the anti-codon for the corresponding codon in the mRNA presented in the A ... When a stop codon is reached, the peptidyl-tRNA bond of the tRNA located in the P-site is cleaved releasing the newly ... Translation moves the tRNA from the A-site through the P- and E-sites, with the exception of the initiator tRNA, which binds ...
Reelin
ATG initiator codon of the RELN gene in an Italian population. Longer triplet repeats in the 5' region were associated with an ...
Index of genetics articles
Industrial melanism Infectious transfer Informed consent Inherit Inherited Initiation codon Initiation Initiation Initiator ... bank Cloned DNA Cloning Cloning vector Coccus Code Code dictionary Coding strand Codominance Codon Codon usage bias aka Codon ... Ochre codon Okazaki fragment Oligo Oligogenic Oligonucleotide Oncogene Oncogenes Oncovirus Oocyte Oogenesis Oogonia Opal codon ... Non-disjunction Non-histone protein Non-linear tetrad Non-Mendelian ratio Non-parental Non-recombinant Nonsense codon Nonsense ...
Parathyroid hormone-related protein
... in-frame and downstream of the initiator AUG codon, to give rise to nuclear forms of this hormone. The protein was first ...
List of MeSH codes (D13)
... codon MeSH D13.444.735.544.355.225 - codon, initiator MeSH D13.444.735.544.355.250 - codon, terminator MeSH D13.444.735.544. ... 355.250.235 - codon, nonsense MeSH D13.444.735.544.500 - rna caps MeSH D13.444.735.544.500.710 - rna cap analogs MeSH D13.444. ...
Biosynthesis
In all, there are 64 codons, 61 of each code for one of the 20 amino acids, while the remaining codons specify chain ... The binding of a charged initiator tRNA into the P site of the ribosome 3. The proper alignment of the ribosome with mRNA's ... The last stage of translation occurs when a stop codon enters the A site. Then, the following steps occur: 1. The recognition ... Biology portal Technology portal Lipids Phospholipid bilayer Nucleotides DNA DNA replication Proteinogenic amino acid Codon ...
Microviridae
Alteration of the ATG start codon of the A protein of bacteriophage phi X174 into an ATT codon yields a viable phage indicating ... an initiator of DNA replication. Nature 288(5791) 561-566 van Mansfeld AD, van Teeffelen HA, Baas PD, Jansz HS (1987) Two ...
Eukaryotic initiation factor
... along the mRNA to reach an AUG start codon. Recognition of the start codon by the Met-tRNAiMet promotes gated phosphate and ... eIF2 is the main protein complex responsible for delivering the initiator tRNA to the P-site of the preinitiation complex, as a ... In particular, eIF1 dissociation from the 40S subunit is considered to be a key step in start codon recognition. eIF1 and eIF1A ... Once the AUG start codon is recognized and located in the P-site, eIF5 stimulates the hydrolysis of eIF2-GTP, effectively ...
Translational regulation
Bases downstream the stop codon affect the activity of these release factors. In fact, some bases proximal to the stop codon ... Hartz D, McPheeters DS, Gold L. Selection of the initiator tRNA by Escherichia coli initiation factors. Genes Dev. 1989;3:1899- ... Once a termination codon is read, release factors RF-1, RF-2, and RF-3 contribute to the hydrolysis of the growing polypeptide ... This is possible due to the matching of 2 out 3 bases within the stop codon by tRNAs that may occasionally outcompete release ...
Contido GC, a enciclopedia libre
Wuitschick JD, Karrer KM (1999). "Analysis of genomic G + C content, codon usage, initiator codon context and translation ...
N-terminus
Since the start codon of the genetic code codes for the amino acid methionine, most protein sequences start with a methionine ( ... Modifications include the removal of initiator methionine (iMet) by aminopeptidases, attachment of small chemical groups such ...
Exon shuffling
... between the first and second nucleotide of a codon (phase 1 introns), or between the second and third nucleotide of a codon ( ... Helitron encoded proteins are composed of a rolling-circle (RC) replication initiator (Rep) and a DNA helicase (Hel) domain. ... Introns can interrupt the reading frame of a gene by inserting a sequence between two consecutive codons (phase 0 introns), ...
Fungal prion
This suggests that these prion domains are, in fact, portable and are the sole initiator of prionogenesis. This supports the ... leading to more frequent stop codon read-through and the development of novel phenotypes. With over 20 prion-like domains ...
Stringent response
"Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP ... and pentaphosphate requires the presence of a codon-specific, uncharged transfer ribonucleic acid in the acceptor site of ...
Archaeal initiation factors
The principal functions these proteins perform include ribosome RNA/mRNA recognition, delivery of the initiator Met-tRNAiMet, ... these TIFs help correct the identification of the initiation codon, while its function is unknown in bacteria. Just between ...
Albert Hofman
Hofman is the initiator and principal investigator of two population-based, prospective cohort studies in the city of Rotterdam ... Presenile-dementia and cerebral- hemorrhage linked to a mutation at codon-692 of the beta-amyloid precursor protein gene. Nat ...
EIF4A
Once bound to the 5' cap of mRNA, this 48S complex then searches for the (usually) AUG start codon and translation begins. In ... Eukaryotic initiation factor complex 2 (eIF2) forms a ternary complex with GTP and the initiator Met-tRNA - this process is ...
Epitranscriptome
... it acts more like a near-cognate codon interaction instead of the cognate codon interaction. This can be seen in the delay in ... such as separating the initiator tRNAMet from elongator tRNAMet.. Moreover, they increase overall tRNA stability. Some studies ... All eukaryotic stop codons contain one uridine (UAA, UGA and UGA); conversion of this uridine to pseudouridine results in ... Secondly, this mark is enriched in specific regions of the transcriptome; it is mostly found close to stop codons, in 3'-UTRs ...
Eukaryotic chromosome fine structure
... and an initiator. Exons are the part of the transcript that will eventually be transported to the cytoplasm for translation. ... region downstream from the stop codon is separated into two parts: 3' UTR is never translated, but serves to add mRNA stability ...
Kasugamycin
Instead, kasugamycin mimics the codon nucleotides at the P and E sites by binding within the path of the mRNA, thus perturbing ... Kasugamycin inhibition is thought to occur by direct competition with initiator transfer RNA. Recent experiments suggest that ... the mRNA-tRNA codon-anticodon interaction. Low level resistance to kasugamycin is acquired by mutations in the 16S rRNA ...
EF-Tu
... in which the anticodon of the tRNA binds to the codon of the mRNA. If the correct anticodon binds to the mRNA codon, the ... in both EF-1alpha/EF-Tu and also in EF-2/EF-G and thus seems typical for GTP-dependent proteins which bind non-initiator tRNAs ... Messenger RNA (mRNA) carries the genetic information that encodes the primary structure of a protein, and contains codons that ... In translation, a fundamental problem is that near-cognate anticodons have similar binding affinity to a codon as cognate ...
Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. -...
By analyzing the effects of single base substitutions around the ATG initiator codon in a cloned preproinsulin gene, I have ... Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes.. Kozak M ... A purine in position -3 (i.e., 3 nucleotides upstream from the ATG codon) has a dominant effect; when a pyrimidine replaces the ... The mechanism by which nucleotides flanking the ATG codon might exert their effect is discussed. ...
Translation Initiation in Drosophila melanogaster Is Reduced by Mutations Upstream of the AUG Initiator Codon<...
Translation Initiation in Drosophila melanogaster Is Reduced by Mutations Upstream of the AUG Initiator Codon. Molecular and ... Translation Initiation in Drosophila melanogaster Is Reduced by Mutations Upstream of the AUG Initiator Codon. / Feng, Yue; ... title = "Translation Initiation in Drosophila melanogaster Is Reduced by Mutations Upstream of the AUG Initiator Codon", ... T1 - Translation Initiation in Drosophila melanogaster Is Reduced by Mutations Upstream of the AUG Initiator Codon ...
LOC366309 (similar to suppressor of initiator codon mutations, related sequence 1) - Chinchilla Research Resource Database
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis
A single sequence context cannot satisfy all non-AUG initiator codons in yeast† | BMC Microbiology | Full Text
We next tested whether the non-AUG initiator codons identified above can also act as initiator codons in GRS1. To this end, the ... it was interesting to point out that the non-AUG initiator codons of ALA1 and GRS1 and the cryptic initiator codon of ALA1 ... a less-efficient non-AUG initiator codon in the context of ALA1, was one of the strongest non-AUG initiator codons in the ... Codon PositionInitiator CodonFusion ConstructSequence ContextAlternative Translation Initiation. Background. Aminoacyl-tRNA ...
Mouse Genomes Project - Query SNPs, indels or SVs - Wellcome Sanger Institute
"Analysis of Genomic G + C Content, Codon Usage, Initiator Codon Contex" by Jeffrey D. Wuitschick and Kathleen M. Karrer
We analyzed G + C content, codon usage, initiator codon context and stop codon sites in the extremely A + T rich genome of this ... Regions immediately preceding Tetrahymena translation initiator codons were generally A-rich. For the 60 stop codons examined, ... the 75 available T. thermophila protein coding sequences favored codons ending in T and, where possible, avoided those with G ... Highly expressed genes were relatively G + C-rich and exhibited an extremely biased pattern of codon usage while ...
The vitamin D receptor gene start codon polymorphism: a functional analysis of FokI variants
... which is three codons upstream of a second start site (ATG). The SCP genotype can be determined with the restriction enzyme ... The vitamin D receptor (VDR) gene contains a start codon polymorphism (SCP) which is three codons upstream of a second start ... Codon, Initiator * Receptors, Calcitriol * DNA Grant support * DK-02459/DK/NIDDK NIH HHS/United States ... The vitamin D receptor gene start codon polymorphism: a functional analysis of FokI variants J Bone Miner Res. 1998 Nov;13(11): ...
Pathophysiology
Oogenesis requires germ cell-specific transcriptional regulators Sohlh1 and Lhx8 | PNAS
Variant Annotation Integrator
initiator_codon_variant. A codon variant that changes at least one base of the first codon of a transcript. ... initiator_codon_variant, incomplete_terminal_codon_variant, stop_lost, stop_retained_variant, stop_gained, NMD_transcript_ ... incomplete_terminal_codon_variant. A sequence variant where at least one base of the final codon of an incompletely annotated ... A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened ...
MEDLINE - Resultado p gina 1
0 (Codon, Initiator); 0 (Genetic Markers). [Em] M s de entrada:. 1705. ... Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted ... using Start Codon Targeted (SCoT) markers. Two cultivated varieties and two wild accessions were evaluated using five SCoT ...
Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications |...
Codon usage pattern. Most protein-coding genes employed the standard initiator codon AUG; however, six unusual start codons ... the codon usage patterns were determined for 71 distinct protein-coding genes in Sect. Marmorata chloroplast genomes. Codons of ... Wright F. The effective number of codons used in a gene. Gene. 1990;87(1):23-9.PubMedGoogle Scholar ... Codon usage and substitution rate calculation. RSCU, GC3s, and ENc for 71 protein-coding genes were calculated using CodonW ...
Animal virus schemes for translation dominance. - PubMed - NCBI
The AUG codon basepairs with the initiator tRNA delivered by eIF2. eIF4GI binding is stimulated by eIF4A and modulated by PTB, ... eIF2 delivers the initiator methionyl tRNA as a ternary complex, comprised of eIF2•GTP•met-tRNAimet. The 40S ribosomal subunit ... The HCV pseudoknot (shaded in grey) positions the initiation codon (green box) in the mRNA binding cleft of the 40S subunit [] ... then scans to locate the AUG codon where the 60S joins, some factors are ejected including eIF2, and the 80S ribosome enters ...
DHCR7 Gene - GeneCards | DHCR7 Protein | DHCR7 Antibody
RPS26 Gene - GeneCards | RS26 Protein | RS26 Antibody
Lrpprc - Leucine-rich PPR motif-containing protein, mitochondrial precursor - Mus musculus (Mouse) - Lrpprc gene & protein
Patent US7300772 - BMP products - Google Patents
Reconstruction of the first eight codons is accomplished by ligation to oliognucleotides: EcoRI Initiator BsmI. ... This deletes all of the sequences 3′ to the translation terminator codon of the BMP-4 cDNA, juxtaposing this terminator codon ... The protein is preceded by a 5′ untranslated region of 342 bp with stop codons in all frames. The 13 bp region preceding this 5 ... Because the genetic code is degenerate (more than one codon can code for the same amino acid), the number of oligo-nucleotides ...
Marilyn Kozak - Wikipedia
Kozak, M (31 January 1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by ... Kozak, M (January 1986). "Point mutations define a sequence flanking the AUG initiator codon that modulates translation by ... Kozak, M (1981). "Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes". ... Kozak, Marilyn (1981-10-24). "Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ...
Nucleotide sequence of tobacco mosaic virus RNA | PNAS
Patente WO1999052357A1 - Assays for inhibitors of bacterial translation initiation factor 3 - Google Patentes
The figure is a schematic diagram of the pAUU-CAT reporter gene construct in which the CAT gene has its ATG initiator codon ... and is based on the ability of IF3 to discriminate against translation initiation at the atypical start codon of the reporter ... 15 the first codon of the reporter gene is an atypical start codon. To make a test strain, the native ATG start codon of a ... The figure is a schematic diagram of the pAUU-CAT reporter gene construct in which the CAT gene has its ATG initiator codon ...
TEAD4 - Transcriptional enhancer factor TEF-3 - Homo sapiens (Human) - TEAD4 gene & protein
Invertebrate mitochondrial code - Wikipedia
... a new initiator codon in vertebrate mitochondrial genome". Nucleic Acids Research. 16 (13): 6233. doi:10.1093/nar/16.13.6233. ... GUG may possibly function as an initiator in Drosophila. AUU is not used as an initiator in Mytilus "An exceptional mechanism ... Sengupta S, Yang X, Higgs PG (June 2007). "The mechanisms of codon reassignments in mitochondrial genetic codes". Journal of ... The codon AGG is absent in Drosophila. AUA, AUU AUC: Apis GUG: Polyplacophora UUG: Ascaris, Caenorhabditis. Nematoda: Ascaris, ...
Ubuntu Manpage:
Bio::Tools::CodonTable - Codon table object
The only differences are in available initiator codons. NCBI Genetic Codes home page: (Last update of the Genetic Codes: April ... codon is_ter_codon Title : is_ter_codon Usage : $obj-,is_ter_codon(GAA) Function: returns true (1) for all codons that can be ... codon unambiguous_codons Title : unambiguous_codons Usage : @codons = $self-,unambiguous_codons(ACN) Returns : array of ... Example : $myCodonTable-,is_ter_codon(ATG) Returns : boolean Args : codon is_unknown_codon Title : is_unknown_codon Usage : $ ...
NADP Transhydrogenase
- Transhydrogenase
Summary Report | CureHunter
Structure, Expression, and Function of ICAM-5
An in-frame termination codon TAG locates 54 nucleotides upstream of the initiator ATG. The human ICAM-5 gene is composed of 11 ... for a strong initiator element [8]. This initiator sequence has been proposed to function as an alternate TFIID-binding site in ... Analysis of the promoter region of the mouse ICAM-5 gene revealed a consensus strong initiator element for TATA-fewer genes, ... This indicates that nucleotides 92-95 bp upstream from the start codon are potential transcription initiation site of the mouse ...
BSI Lecture 5-6 Transcription/Translation Flashcards by Tyler Boyd | Brainscape
The A-site in translation is the entrance for tRNA to be tested for codon/anti-codon match with mRNA. ... 5 UTR is the region of a mRNA that is directly upstream of the initiation codon. 3 UTR is the region that directly follows ... The ability of one tRNA with a specific anticodon to complementary base pair with more than one codon. Matching the 1st and 2nd ... Once the small subunit reaches start codon, eIFs dissociate to all the large subunit to assemble with tRNAiMet in which site? ...
RXs Drugstore: Brianza biblioteche FDA Approved!
New Parvovirus in Child with Unexplained Diarrhea, Tunisia - Volume 20, Number 11-November 2014 - Emerging Infectious Diseases...
The methionine codon of VP2 was located upstream of glycine-rich sequence (GGGARAGGVG). An unusual serine-rich sequence ( ... We also identified 2 conserved replication initiator motifs 127EFHIHVLLW135 and 187VLQYKHSQTR196. Potential splicing signals to ... which we selected as the start codon. The Walker loop 396GPATTGKS403 [GXXXXGK(T/S)], which is an ATP- or GTP-binding motif, was ... Tusavirus has a potential upstream start codon MSS in a weaker Kozak consensus sequence than MAQ (Figure, panel A), ...
PPT - PROTEIN SYNTHESIS PowerPoint presentation | free to download - id: 3dec9c-YzFhZ
The initiator tRNA can then bind to the complex at the P site paired with AUG codon.. 30S initiation complex. The 50S subunits ... Initiators tRNA 4. Codon-anticodon interaction* In the cleft of the ribosome, an anti-parallel formation of three base pairs ... AUG (GUG) start codons in prokaryotes and eukaryotes. *Initiator tRNAs differ from the one that inserts internal Met residues. ... with stop codon and cause release of completed polypeptide chain.. RF1 and RF2 recognizes the stop codon with the help of RF3. ...
MRNATRNARibosomeMethionineAnticodonAmino acidsEukaryoticNucleotides upstreamStartUpstream from the ATG codonSequencesTripletsSubunitTranslationalGenesDownstreamFMet-tRNAfMetProtein synthesisReadthroughRecognitionPeptideDifferProkaryoticEukaryotesContextConstructTripletSTABILITYDrosophilaAlternative translation initiationEfficiencySiteStopGenetic codeBoundBias
MRNA42
- If the first AUG codon is mutated, then initiation can begin at the next available AUG from the 5' end of mRNA. (beds.ac.uk)
- AUU is not used as an initiator in Mytilus "An exceptional mechanism must operate for initiation of translation of the cytochrome oxidase subunit I mRNA in both D. melanogaster and D. yakuba, since its only plausible initiation codon, AUA, is out of frame with the rest of the gene. (wikipedia.org)
- The A-site in translation is the entrance for tRNA to be tested for codon/anti-codon match with mRNA. (brainscape.com)
- In the cleft of the ribosome, an anti-parallel formation of three base pairs occurs between the codon on the mRNA and the anticodon on the tRNA. (powershow.com)
- the anticodon base-pairs with a complementary codon on mRNA and (abbreviated tRNA and formerly referred to as sRNA , for soluble RNA [1] ) is an adaptor molecule composed of RNA , typically 76 to 90 nucleotides in length, [2] that serves as the physical link between the mRNA and the amino acid sequence of proteins. (wikipedia.org)
- tRNA does this by carrying an amino acid to the protein synthetic machinery of a cell ( ribosome ) as directed by a 3-nucleotide sequence ( codon ) in a messenger RNA (mRNA). (wikipedia.org)
- [3] The mRNA encodes a protein as a series of contiguous codons, each of which is recognized by a particular tRNA. (wikipedia.org)
- The anticodon forms three complementary base pairs with a codon in mRNA during protein biosynthesis. (wikipedia.org)
- 20. The last codon in a mRNA molecule that specifies the end of a protein molecule is known as a ____________codon. (majortests.com)
- instead, Ksg mimics codon nucleotides at the P and E sites by binding within the path of the mRNA. (sigmaaldrich.com)
- Coupled with biochemical experiments, our results suggest that Ksg indirectly inhibits P-site tRNA binding through perturbation of the mRNA-tRNA codon-anticodon interaction during 30S canonical initiation. (sigmaaldrich.com)
- Two possible non-AUG initiation codons, CUG and ACG, are present in the 5′ region of AG mRNA preceding the highly conserved MADS box sequence. (asm.org)
- The recognition by eukaryotic ribosomes of the translation initiation codon generally proceeds by a scanning mechanism in which the 40S ribosomal subunit migrates from the 5′ end of the mRNA molecule, stopping at the first AUG triplet that is found in a favorable sequence context for initiation of translation ( 25 , 27 , 31 ). (asm.org)
- Most of the cases so far described in which a non-AUG codon acts as the start site for eukaryotic mRNA translation are analogous to translation by leaky scanning ( 27 ), in that two different protein products are produced: the synthesis of one polypeptide is initiated at the non-AUG codon, and another is synthesized from a downstream AUG, usually in frame with the non-AUG codon. (asm.org)
- Equine infectious anemia virus Tat protein is synthesized by initiation at a CUG codon, which is bypassed by some ribosomes (leaky scanning), allowing translation of the downstream rev cistron of the bicistronic tat-rev mRNA ( 8 ). (asm.org)
- 1-In Nirenberg's experiment (building a protein from mRNA made only of U-U-U-U-U ...), how was the protein actually built if it didn't start with AUG (the starting Codon). (physicsforums.com)
- Translation of a Pro‐Pro‐Gly peptide sequence juxtaposed to the uORF2 stop codon results in ribosome dissociation from the mRNA and causes low levels of GADD34 expression. (els.net)
- The nucleotide sequence in mRNA is recognized in triplets, called codons. (news-medical.net)
- The ribosome moves along the single strand mRNA, and when a complimentary codon sequence belonging to amino acid bearing tRNA bonds with the mRNA, the amino acid is added to the chain. (news-medical.net)
- The mRNA possesses a stop codon, a sequence of three nucleotides that indicates that translation is complete. (news-medical.net)
- Upon reaching the stop codon, the ribosome ceases translation and releases the mRNA and newly generated polypeptide. (news-medical.net)
- Strands of mRNA are made up of codons, each of which signifies a particular amino acid to be added to the polypeptide in a certain order. (news-medical.net)
- mRNA must interact with ribosomal RNA (rRNA), the central component of ribosomal machinery that recognizes the start and stop codons of mRNA, and tRNA, which provides the amino acid once bound with a complimentary mRNA codon. (news-medical.net)
- Each tRNA is read as a ribonucleotide triplet called an anticodon that is complementary to an mRNA codon. (news-medical.net)
- The initiator tRNA which is equipped with the anticodon (UAC) also binds to the start codon (AUG) of the mRNA. (news-medical.net)
- If the anticodon of the new tRNA matches the mRNA codon, base pairing occurs and the two amino acids are linked by the ribosome through a peptide bond. (news-medical.net)
- As the ribosome moves along the mRNA, it encounters one of the three stop codons for which there is no corresponding tRNA. (news-medical.net)
- Translation initiation is a complex process in which the initiator tRNA and the 40S and 60S ribosomal subunits are recruited to the 5′ end of a mRNA molecule and assembled by eukaryotic translation initiation factors into an 80S ribosome at the start codon of the mRNA (Fig. 1) . (aacrjournals.org)
- The 43S initiation complex (40S/eIF2/Met-tRNA/GTP complex) scans the mRNA in a 5′→3′ direction until it encounters an AUG start codon. (aacrjournals.org)
- Codon and amino acid content are associated with mRNA stability in mammalian cells 2020-02-13 00:00:00 a1111111111 a1111111111 Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in the a1111111111 cell and is a major control point for modulating gene expression. (deepdyve.com)
- Herein we characterize the contribution of coding sequence towards TJ, Hanson G, Coller J (2020) Codon and amino mRNA decay in human and Chinese Hamster Ovary cells. (deepdyve.com)
- In agreement with previous stud- acid content are associated with mRNA stability in ies, we observed that synonymous codon usage impacts mRNA stability in mammalian cells. (deepdyve.com)
- The impact of codon and amino acid identity Editor: Yoon Ki Kim, Korea University, REPUBLIC on mRNA decay appears to be associated with underlying tRNA and intracellular amino acid OF KOREA concentrations. (deepdyve.com)
- Accordingly, genes of similar physiological function appear to coordinate Received: December 5, 2019 their mRNA stabilities in part through codon and amino acid content. (deepdyve.com)
- i) The termination codon of a uORF can be recognised as premature and nonsense‐mediated mRNA decay ( NMD ) is triggered through a mechanism involving the UPF1 protein and ribonucleases. (els.net)
- p97 mRNA has no initiator AUG and translation starts exclusively at a GUG codon. (embl-heidelberg.de)
- During initiation , the ribosome is assembled at the initiation codon in the mRNA with a methionyl initiator tRNA bound in the peptidyl (P) site. (hindawi.com)
- The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. (rcsb.org)
- Each three mRNA nucleotides are called a codon and their three complementary tRNA nucleotides are called its anti-codon . (academickids.com)
- Initiation of translation involves the small ribosomal subunit binding to the 'start' codon on the mRNA, which indicates where the mRNA starts coding for the protein. (academickids.com)
- During the elongation phase, amino acids are added to the nascent peptide chain in accordance with codon sequences in the mRNA. (asnjournals.org)
- Translation of mRNA, the process by which codon sequences in mRNA are used to synthesize a polypeptide chain, has received scant attention. (asnjournals.org)
TRNA13
- Previous studies in Saccharomyces cerevisiae showed that ALA1 (encoding alanyl-tRNA synthetase) and GRS1 (encoding glycyl-tRNA synthetase) respectively use ACG and TTG as their alternative translation initiator codons. (beds.ac.uk)
- However, two Saccharomyces cerevisiae genes, HTS1 (the gene encoding histidyl-tRNA synthetase) [ 6 ] and VAS1 (the gene encoding valyl-tRNA synthetase (ValRS)) [ 7 ], specify both the mitochondrial and cytosolic forms through alternative translation initiation from two in-frame AUG codons. (beds.ac.uk)
- The AUG codon basepairs with the initiator tRNA delivered by eIF2. (nih.gov)
- Only the initiator methionyl-tRNA is modified by transformylase to give N-formylmethionyl-tRNAfmet. (powershow.com)
- The initiator tRNA can then bind to the complex at the P site paired with AUG codon. (powershow.com)
- Because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing different anticodons which carry the same amino acid. (wikipedia.org)
- Base‐pairing between the start codon and the anti‐codon of the tRNA i Met at the P‐site promotes conformational changes within the PIC, with the consequent release of Pi, eIF1, and eIF2‐GDP in complex with eIF5. (els.net)
- tRNA carry a particular amino acid, which is added to the growing polypeptide chain if complimentary codons bond. (news-medical.net)
- Following initiation, a new tRNA-amino acid complex enters the codon next to the AUG codon. (news-medical.net)
- If the anticodon does not match the codon, base pairing cannot happen and the tRNA is rejected. (news-medical.net)
- Then, the ribosome moves one codon forward making space for a new tRNA-amino acid complex to enter. (news-medical.net)
- This start codon is then base-paired to the anticodon of initiator tRNA, forming the 48S initiation complex. (aacrjournals.org)
- The initiator tRNA charged with Met forms part of the ribosomal complex. (academickids.com)
Ribosome3
- Terminator proteins present at the stop codon bind to the ribosome and trigger the release of the newly synthesized polypeptide chain. (news-medical.net)
- Also, the uORF nucleotide sequence can have a role on its translation efficiency, for instance by encoding rare codons that cause the ribosome to stall. (els.net)
- This procedure repeats until the ribosome encounters one of three possible stop codons, where translation is terminated. (academickids.com)
Methionine3
- AUG is an initiator codon i.e. it initiates the translation process & also codes for methionine. (jagranjosh.com)
- In eukaryotes and archaea , the amino acid encoded by the start codon is methionine . (academickids.com)
- The stretch of bases from the cap to the first methionine (AUG) codon is not translated and is called the 5′ untranslated region (UTR). (asnjournals.org)
Anticodon1
- The weakened codon-anticodon interaction, however, might be compensated for by contacts with nearby nucleotides, since translation initiation at non-AUG codons requires that such codons be in an optimal or favorable sequence context ( 28 , 33 ). (asm.org)
Amino acids3
- It provides methods to output information about tables and relationships between codons and amino acids. (ubuntu.com)
- Note: This class deals primarily with individual codons and amino acids. (ubuntu.com)
- The 5′UTR is succeeded by the coding sequence of bases, which in triplets form codons that carry the genetic message for individual amino acids. (asnjournals.org)
Eukaryotic6
- Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. (nih.gov)
- By analyzing the effects of single base substitutions around the ATG initiator codon in a cloned preproinsulin gene, I have identified ACCATGG as the optimal sequence for initiation by eukaryotic ribosomes. (nih.gov)
- An AUG codon indeed serves as the translation start site in the vast majority of eukaryotic genes, but evidence accumulated over the past years indicates that the translation of several animal and viral mRNAs can be or is initiated at codons which differ from AUG in one base, like CUG, ACG, and GUG ( 17 , 28 ). (asm.org)
- Eukaryotic cellular mRNAs whose translation is initiated exclusively at a non-AUG codon, however, are rare. (asm.org)
- 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)
- 1994 ) The immediate downstream codon strongly influences the efficiency of utilization of eukaryotic translation initiation codons. (biologists.org)
Nucleotides upstream2
- There are two major transcription initiation sites that are located at 215 and 188 nucleotides upstream of the initiator codon. (stanford.edu)
- These sequences lie about 10 nucleotides upstream from the AUG start codon. (thermofisher.com)
Start15
- Single base substitutions around an upstream, out-of-frame ATG codon affect the efficiency with which it acts as a barrier to initiating at the downstream start site for preproinsulin. (nih.gov)
- The importance to in vivo translation of sequences immediately upstream of the Drosophila alcohol dehydrogenase (Adh) start codon was examined at two developmental stages. (elsevier.com)
- The vitamin D receptor (VDR) gene contains a start codon polymorphism (SCP) which is three codons upstream of a second start site (ATG). (nih.gov)
- Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers. (bireme.br)
- Here, we investigate the optimal number of individuals that may represent the genetic diversity of a single population, using Start Codon Targeted (SCoT) markers. (bireme.br)
- The assay uses a reporter gene system in whole cells, and is based on the ability of IF3 to discriminate against translation initiation at the atypical start codon of the reporter gene. (google.es)
- Initiator tRNAs are special tRNAs recognizing the AUG (GUG) start codons in prokaryotes and eukaryotes. (powershow.com)
- Numbering is relative to the first nucleotide of the start codon. (nih.gov)
- (15) identified two polymorphisms at the 5′ noncoding region (A23G, at position −4 from the ATG start codon) and codon 228 (G709A, in exon 6) in the XPA gene. (aacrjournals.org)
- Anyway, the point is that the protein was made although the RNA did not start with AUG (the starting codon). (physicsforums.com)
- b) During basal conditions, scanning ribosomes bypass the GADD34 uORF1 due to its poor start codon context and initiate translation at uORF2. (els.net)
- Translation is generally linear from the initiating start to the terminating stop codon of an open reading frame (ORF). (asm.org)
- Heterologous expression of the trp(G.D) and trpC genes in E.coli and N-terminal sequencing of their polypeptide products showed that their translation is initiated at the rate start codons TTG and ATC, respectively. (uni-regensburg.de)
- Furthermore, our experiments demonstrate that two isoforms of Oskar protein are produced by alternative start codon usage. (biologists.org)
- This codon is most commonly an AUG, but alternative start codons are common in prokaryotes . (academickids.com)
Upstream from the ATG codon1
- The putative transcription site was present 192 bp upstream from the ATG codon. (embl-heidelberg.de)
Sequences1
- the 75 available T. thermophila protein coding sequences favored codons ending in T and, where possible, avoided those with G in the third position. (marquette.edu)
Triplets3
- To explore if any other non-ATG triplets can act as initiator codons in yeast, ALA1 was used as a reporter for screening. (beds.ac.uk)
- We show herein that except for AAG and AGG, all triplets that differ from ATG by a single nucleotide were able to serve as initiator codons in ALA1 . (beds.ac.uk)
- These results indicate that translation of AG is initiated exclusively at an ACG codon and prove that non-AUG triplets may be efficiently used as the sole translation initiation site in some plant cellular mRNAs. (asm.org)
Subunit1
- For a uORF to function as a translational regulatory element, its initiation codon must be recognised, at least at certain times, by the scanning 40S ribosomal subunit and associated translation initiation factors. (els.net)
Translational3
- The number of uORFs, the intercistronic distance, the overlap with the mORF and the context of the initiation codon are the uORF‐related structural features that most influence their translational regulatory capacity. (els.net)
- Here we review the basic principles of translational control, the alterations en countered in cancer, and selected therapies targeting translation initiation to elucidate potential new therapeutic avenues. (aacrjournals.org)
- 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)
Genes3
- Highly expressed genes were relatively G + C-rich and exhibited an extremely biased pattern of codon usage while developmentally regulated genes were more A + T-rich and showed less codon usage bias. (marquette.edu)
- Additionally, almost all the plastid protein coding genes were found to prefer ending with A/U. Mutation bias and selection pressure predominately shaped the codon bias of most genes. (springer.com)
- Mutation and natural selection were the main forces to drive the codon bias pattern of most plastid protein coding genes. (springer.com)
Downstream1
- However, a similar mutation of the downstream ACG codon prevents the rescue of the ag-3 mutant phenotype. (asm.org)
FMet-tRNAfMet1
- The +1 A is the first base of the AUG initiator codon (shaded) responsible for binding of fMet-tRNAfMet. (thermofisher.com)
Protein synthesis1
- 1994 ) Positions +5 and +6 can be major determinants of the efficiency of non-AUG initiation codons for protein synthesis. (biologists.org)
Readthrough2
- Overlapping the terminal five codons of this readthrough reading frame is a second reading frame coding for a protein of Mr 29,987. (pnas.org)
- Recoding events include programmed ribosomal frameshift and stop codon readthrough, used extensively by viruses but also during translation of a number of cellular mRNAs to generate certain proteins or protein variants. (asm.org)
Recognition1
- Further, high-level expression of a 2A peptide-containing protein inhibits the growth of cells compromised for release factor activity and leads to errors in stop codon recognition. (asm.org)
Peptide2
- We propose that the nascent 2A peptide interacts with ribosomes to drive a highly unusual and specific "termination" reaction, despite the presence of a proline codon in the A site. (asm.org)
- At its 3′ end, the coding sequence contains a termination codon, which signals ending of peptide chain synthesis. (asnjournals.org)
Differ2
- Initiator tRNAs differ from the one that inserts internal Met residues. (powershow.com)
- Of the 9 possible codons that differ from AUG in a single position, 5 are used to initiate the extensions of the 17 known cases that passed our qualitative analysis for conservation of the extension. (nih.gov)
Prokaryotic1
- Activity of prokaryotic RBSs can be influenced by the length and nucleotide composition of the spacer separating the RBS and the initiator AUG. (thermofisher.com)
Eukaryotes1
- In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5' cap. (nih.gov)
Context4
- In particular, GTG was one of the most efficient non-ATG initiator codons, while ATA was essentially inactive in the context of GRS1 . (beds.ac.uk)
- This finding indicates that a sequence context that is favorable for a given non-ATG initiator codon might not be as favorable for another. (beds.ac.uk)
- We analyzed G + C content, codon usage, initiator codon context and stop codon sites in the extremely A + T rich genome of this ciliate. (marquette.edu)
- In addition to the identity of the initiation codon, the initiation context of the 17 previously known examples that passed the screening process and the 42 newly identified candidates were examined (Figure 6). (nih.gov)
Construct2
- The figure is a schematic diagram of the pAUU-CAT reporter gene construct in which the CAT gene has its ATG initiator codon replaced with ATT. (google.es)
- Conversely, if an ATG is introduced immediately 5′ to the disrupted ACG codon, the resulting construct fully complements the ag-3 mutation. (asm.org)
Triplet1
- AG cDNA contains an open reading frame that lacks an ATG triplet to function as the translation initiation codon, and the actual amino terminus of the AG protein remains uncharacterized. (asm.org)
STABILITY1
- In yeast and other model organisms, codon identity is a powerful determinant of transcript stability, contributing broadly to impact half-lives. (deepdyve.com)
Drosophila1
- GUG may possibly function as an initiator in Drosophila. (wikipedia.org)
Alternative translation initiation1
- We hypothesized that alternative translation initiation from four AUG codons corresponding to amino acid positions 1, 5, 16, and 33 could produce the observed RGS2 expression profile. (aspetjournals.org)
Efficiency1
- This order correlates with the efficiency of initiation for each non-AUG codon, with CUG the most efficient of them all (16). (nih.gov)
Site3
- For the 60 stop codons examined, the frequency of G in the end + 1 site was much higher than expected whereas C never occupied this position. (marquette.edu)
- Alteration of the CTG codon to render it unsuitable for acting as a translation initiation site does not affect complementation of the ag-3 mutation in transgenic plants. (asm.org)
- We need to find a new vector with a bacterial ribosyme binding site, initiator, and a stop codon. (igem.org)
Stop1
- What are the stop codons? (brainscape.com)
Genetic code1
- Several arthropods translate the codon AGG as lysine instead of serine (as in the Pterobranchia Mitochondrial Code) or arginine (as in the standard genetic code). (wikipedia.org)
Bound1
- When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). (proteopedia.org)
Bias1
- The distribution of the putative initiation codons of the 42 new candidates in humans is not radically different (notwithstanding the potential for observer bias in locating the precise initiation codon in a small number of cases). (nih.gov)